[T-Mobile Samsung Galaxy Note II] incalescence:
I've only lurked on here for years, since I rarely have anything of value to add. In the event this is helpful to anyone, here's my experience:

(As an added note, I do have the ISIS SIM as well - number of Secure Elements: 2, per logcat)

D/NFCJNI (12025): phLibNfc_SE_GetSecureElementList()

D/NFCJNI (12025):

D/NFCJNI (12025): > Number of Secure Element(s) : 2

D/NFCJNI (12025): phLibNfc_SE_SetMode() returned 0x000d[NFCSTATUS_PENDING]

D/STATUSBAR-NotificationService( 2410): Noti Alert - mSystemReady:true, AlertEnabled:true

I/NFCJNI (12025): duration = 500000

I/NFCJNI (12025): NFC Initialized

D/NFCJNI (12025): phLibNfc_SE_GetSecureElementList(): SMX detected

D/NFCJNI (12025): phLibNfc_SE_GetSecureElementList(): UICC detected

Rooted stock rom

Flashed the libs from the first post

Wallet from the market didn't seem to work

Used the modified Wallet from Modaco - got to the same point mentioned in the OP

Changed my build.prop values to "htc_jewel" for all

Got further after a VERY long delay

All of my credit card information from previous purchase on Play Market showed up (which did not show prior), but had a warning

Clicked this warning, and it said it had to reset Google Wallet

Proceeded to reset Google Wallet (longest reset it had done in my attempts)

Attempted to add either of my google accounts again, and it just hung at the adding account - never prompted for password as on previous attempts

Tried full reset and numerous roms with no change in the behavior

Tried downloading Wallet from the market again, and now I am seeing errors in logcat - tried with the modified again and receive the same errors:

E/NfcService( 3215): NFC-EE ON

D/NfcService( 3215): NFC-C ON

I/NfcExecutionEnvironmentManagerImpl( 8551): Wakelock WakeLock{419ae8d8 held=false, refCount=0} released 1353545815145 ms

E/InitializerTaskManagerImpl( 8551): CHECK_DATABASE_AND_SECURE_ELEMENT: elapsed=158ms failed: com.google.android.apps.wallet.secureelement.SecureElementAppletStatusException: ControllerAppletImpl: SELECT a0000004762010 expected=0x9000: statusWord=0x6a81 (Function Not Supported)

E/InitializerTaskManagerImpl( 8551): CHECK_DATABASE_AND_SECURE_ELEMENT: waited: failed: com.google.android.apps.wallet.secureelement.SecureElementAppletStatusException: ControllerAppletImpl: SELECT a0000004762010 expected=0x9000: statusWord=0x6a81 (Function Not Supported)

E/InitializerTaskManagerImpl( 8551): CHECK_DATABASE_AND_SECURE_ELEMENT: waited: failed: com.google.android.apps.wallet.secureelement.SecureElementAppletStatusException: ControllerAppletImpl: SELECT a0000004762010 expected=0x9000: statusWord=0x6a81 (Function Not Supported)

E/InitializerTaskManagerImpl( 8551): IDENTIFY_SECURE_ELEMENT: aborting; failedDependencies=[CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): IDENTIFY_SECURE_ELEMENT: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): CHECK_CPLC: aborting; failedDependencies=[CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): INITIALIZE_MIFARE_FORCED: aborting; failedDependencies=[CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): INITIALIZE_MIFARE_FORCED: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): CHECK_CPLC: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): INITIALIZE_MIFARE_FORCED: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT]

E/InitializerTaskManagerImpl( 8551): SCHEDULE_MAINTENANCE_SERVICE: aborting; failedDependencies=[CHECK_DATABASE_AND_SECURE_ELEMENT, INITIALIZE_MIFARE_FORCED]

I/InitializerTaskManagerImpl( 8551): EXPIRE_PIN: starting

E/InitializerTaskManagerImpl( 8551): SCHEDULE_MAINTENANCE_SERVICE: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT, INITIALIZE_MIFARE_FORCED]

I/NfcExecutionEnvironmentManagerImpl( 8551): Wakelock WakeLock{419ae8d8 held=true, refCount=1} acquired 1353545815181 ms

D/KeyguardViewMediator( 2415): setHidden false

D/KeyguardViewMediator( 2415): setHidden false

D/dalvikvm( 6412): GC_FOR_ALLOC freed 482K, 8% free 13980K/15175K, paused 14ms, total 14ms

I/PinProtectedServicesManagerImpl( 8551): mSecureElementManager.disablePayments failed: com.google.android.apps.wallet.secureelement.SecureElementAppletStatusException: ControllerAppletImpl: SELECT a0000004762010 expected=0x9000: statusWord=0x6a81 (Function Not Supported)

I/PinProtectedServicesManagerImpl( 8551): mMifareManager.disableMifareApplications failed: com.google.android.apps.wallet.secureelement.SecureElementAppletStatusException: MifareAppletImpl: SELECT a0000004763030 expected=0x9000: statusWord=0x6a81 (Function Not Supported)

E/NfcService( 3215): NFC-EE ON

D/NfcService( 3215): NFC-C ON

I/NfcExecutionEnvironmentManagerImpl( 8551): Wakelock WakeLock{419ae8d8 held=false, refCount=0} released 1353545815457 ms

I/InitializerTaskManagerImpl( 8551): EXPIRE_PIN: elapsed=301ms finished

I/InitializerTaskManagerImpl( 8551): waited [EXPIRE_PIN]

E/InitializerTaskManagerImpl( 8551): MARK_BOOT_TASKS_COMPLETED: aborting; failedDependencies=[CHECK_DATABASE_AND_SECURE_ELEMENT, CHECK_CPLC, INITIALIZE_MIFARE_FORCED, SCHEDULE_MAINTENANCE_SERVICE]

E/InitializerTaskManagerImpl( 8551): MARK_BOOT_TASKS_COMPLETED: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_DATABASE_AND_SECURE_ELEMENT, CHECK_CPLC, INITIALIZE_MIFARE_FORCED, SCHEDULE_MAINTENANCE_SERVICE]

E/InitializerTaskManagerImpl( 8551): CHECK_BOOT_TASKS_COMPLETE: aborting; failedDependencies=[MARK_BOOT_TASKS_COMPLETED]

E/InitializerTaskManagerImpl( 8551): CHECK_BOOT_TASKS_COMPLETE: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [MARK_BOOT_TASKS_COMPLETED]

E/InitializerTaskManagerImpl( 8551): GET_ENVIRONMENT_INFO: aborting; failedDependencies=[CHECK_BOOT_TASKS_COMPLETE]

E/InitializerTaskManagerImpl( 8551): GET_ENVIRONMENT_INFO: waited: failed: com.google.android.apps.wallet.init.InitializerTaskDependenciesFailedException: [CHECK_BOOT_TASKS_COMPLETE]

Before the seeming success:

I/InitializerTaskManagerImpl( 4022): submitted [CHECK_DATABASE_AND_SECURE_ELEMENT, IDENTIFY_SECURE_ELEMENT, CHECK_CPLC, INITIALIZE_MIFARE_FORCED, SCHEDULE_MAINTENANCE_SERVICE, EXPIRE_PIN, MARK_BOOT_TASKS_COMPLETED, CHECK_BOOT_TASKS_COMPLETE, GET_ENVIRONMENT_INFO, START_PREFETCH_IMAGE_SERVICE, INITIALIZE_MIFARE_IF_NEEDED, INITIALIZE_SHARED_PREFERENCES, START_ACCOUNT_VERIFICATION, ENABLE_CARD_EMULATION, DOWNLOAD_NEW_TOS_DATA_IF_NEEDED, SYNC_WALLET, INITIALIZE_BOTNET, START_BALANCE_FETCHER, SCHEDULE_TSA_C2DM_REGISTRATION_SERVICE, GAIA_ACCOUNT_MISSING_CHECK, SCHEDULE_WALLET_C2DM_REGISTRATION_SERVICE, PREPAID_TURNDOWN_DEPROVISION_PREPAID_AUTOMATICALLY]

I/InitializerTaskManagerImpl( 4022): CHECK_DATABASE_AND_SECURE_ELEMENT: starting

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=true, refCount=1} acquired 1353532065063 ms

I/SurfaceFlinger( 1971): id=22(2) createSurf 0x4005d00c (1x1),1 flag=0, TetupActivi

D/KeyguardViewMediator( 2410): setHidden false

I/SurfaceFlinger( 1971): id=23(2) createSurf (16x16),-1 flag=20000, EimAnimator

D/KeyguardViewMediator( 2410): setHidden false

D/dalvikvm( 3191): GC_CONCURRENT freed 136K, 6% free 12630K/13319K, paused 1ms+3ms, total 27ms

D/KeyguardViewMediator( 2410): setHidden false

D/NfcService( 3191): NFC-C ON

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=false, refCount=0} released 1353532065180 ms

D/SyncManager( 2410): setSyncAutomatically: provider com.google.android.apps.wallet, user 0 -> false

D/SyncManager( 2410): setIsSyncable: , provider com.google.android.apps.wallet, user 0 -> 0

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=true, refCount=1} acquired 1353532065242 ms

D/dalvikvm( 6490): GC_FOR_ALLOC freed 193K, 8% free 13748K/14919K, paused 18ms, total 18ms

W/ResourceType( 4221): getEntry failing because entryIndex 1680 is beyond type entryCount 1631

W/ResourceType( 4221): Failure getting entry for 0x7f020690 (t=1 e=1680) in package 0 (error -2147483647)

W/ResourceType( 4221): getEntry failing because entryIndex 1680 is beyond type entryCount 1631

W/ResourceType( 4221): Failure getting entry for 0x7f020690 (t=1 e=1680) in package 0 (error -2147483647)

D/KeyguardViewMediator( 2410): setHidden false

D/KeyguardViewMediator( 2410): setHidden false

D/NfcService( 3191): NFC-C ON

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=false, refCount=0} released 1353532065473 ms

E/DowngradeSafeSQLiteOpenHelper( 4022): old version: 0 new version: 22

E/Trace ( 7560): error opening trace file: No such file or directory (2)

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=true, refCount=1} acquired 1353532065643 ms

D/dalvikvm( 7560): GC_CONCURRENT freed 159K, 6% free 12409K/13127K, paused 2ms+2ms, total 26ms

D/dalvikvm( 6490): GC_FOR_ALLOC freed 193K, 8% free 13748K/14919K, paused 35ms, total 36ms

D/NfcService( 3191): NFC-C ON

I/NfcExecutionEnvironmentManagerImpl( 4022): Wakelock WakeLock{422a2738 held=false, refCount=0} released 1353532065754 ms

E/TsaRegistrationImpl( 7560): Invalid state: Attempting to re-register.

I/InitializerTaskManagerImpl( 4022): CHECK_DATABASE_AND_SECURE_ELEMENT: elapsed=750ms finished

I/InitializerTaskManagerImpl( 4022): IDENTIFY_SECURE_ELEMENT: starting

At this point, since I wasn't using much that really required root, I decided to just reflash stock rom and see if ISIS would work - it did, not a problem. Of course, I assume it's using the second secure element.

Not sure if this will help out - the next thing I really wanted to try doing was to use the modified APK and the Galaxy Nexus build prop changes since I noticed an "unsupported" message in one of the logcat runs for "htc_jewel" - I would be very curious to see if that works for anyone.