[Nook Touch Android Development] rob.power:
A brief update:

I still need to fix a few things. I'm quite conviced it should work well, but I'm still having invalid digest errors which lead to the apparent boot loop.

[...]
W/PackageParser( 992): Exception reading /system/framework/framework-res.apk
W/PackageParser( 992): java.lang.SecurityException: META-INF/CERT.SF has invalid digest for res/drawable-es-mdpi/c_quicknav_shop_normal_sm.png in /system/framework/framework-res.apk
W/PackageParser( 992):	at java.util.jar.JarVerifier.verifyCertificate(JarVerifier.java:370)
W/PackageParser( 992):	at java.util.jar.JarVerifier.readCertificates(JarVerifier.java:273)
W/PackageParser( 992):	at java.util.jar.JarFile.getInputStream(JarFile.java:416)
W/PackageParser( 992):	at android.content.pm.PackageParser.loadCertificates(PackageParser.java:327)
W/PackageParser( 992):	at android.content.pm.PackageParser.collectCertificates(PackageParser.java:461)
W/PackageParser( 992):	at com.android.server.PackageManagerService.collectCertificatesLI(PackageManagerService.java:2080)
W/PackageParser( 992):	at com.android.server.PackageManagerService.scanPackageLI(PackageManagerService.java:2113)
W/PackageParser( 992):	at com.android.server.PackageManagerService.scanDirLI(PackageManagerService.java:2051)
W/PackageParser( 992):	at com.android.server.PackageManagerService.<init>(PackageManagerService.java:563)
W/PackageParser( 992):	at com.android.server.PackageManagerService.main(PackageManagerService.java:336)
W/PackageParser( 992):	at com.android.server.ServerThread.run(SystemServer.java:120)
I/PackageManager( 992): Failed verifying certificates for package:android
D/PackageManager( 992): Scanning app dir /system/app
I/PackageManager( 992): /system/app/AFfileDownloadService.apk changed; collecting certs
W/PackageParser( 992): Exception reading /system/app/AFfileDownloadService.apk
W/PackageParser( 992): java.lang.SecurityException: META-INF/CERT.SF has invalid digest for classes.dex in /system/app/AFfileDownloadService.apk
W/PackageParser( 992):	at java.util.jar.JarVerifier.verifyCertificate(JarVerifier.java:370)
W/PackageParser( 992):	at java.util.jar.JarVerifier.readCertificates(JarVerifier.java:273)
W/PackageParser( 992):	at java.util.jar.JarFile.getInputStream(JarFile.java:416)
W/PackageParser( 992):	at android.content.pm.PackageParser.loadCertificates(PackageParser.java:327)
W/PackageParser( 992):	at android.content.pm.PackageParser.collectCertificates(PackageParser.java:461)
W/PackageParser( 992):	at com.android.server.PackageManagerService.collectCertificatesLI(PackageManagerService.java:2080)
W/PackageParser( 992):	at com.android.server.PackageManagerService.scanPackageLI(PackageManagerService.java:2113)
W/PackageParser( 992):	at com.android.server.PackageManagerService.scanDirLI(PackageManagerService.java:2051)
W/PackageParser( 992):	at com.android.server.PackageManagerService.<init>(PackageManagerService.java:569)
W/PackageParser( 992):	at com.android.server.PackageManagerService.main(PackageManagerService.java:336)
W/PackageParser( 992):	at com.android.server.ServerThread.run(SystemServer.java:120)
I/PackageManager( 992): Failed verifying certificates for package:com.bn.nook.affiledownloadservice
I/PackageManager( 992): /system/app/Accessories.apk changed; collecting certs
W/PackageParser( 992): Exception reading /system/app/Accessories.apk
W/PackageParser( 992): java.lang.SecurityException: META-INF/CERT.SF has invalid digest for res/drawable/s_icon_recommend.png in /system/app/Accessories.apk
[...]

By the way, when checking on my pc using "jarsigner -verify -verbose" I don't get any errors, just the same warnings I get if I check the original apks.

[ ... ]
This jar contains entries whose certificate chain is not validated.
This jar contains signatures that does not include a timestamp. Without a timestamp, users may not be able to validate this jar after the signer certificate's expiration date (2037-11-20) or after any future revocation date.

I've read around the internet that this could be due to a problem when signing using jdk7, as with this version they changed the default signing algorithm.

I will give it a try installing jdk6 to see if it works. ;)

If somebody has more suggestions about the error, they are welcome. :)