[Atrix 4G Android Development] fboaventura:
I'd got some rare spare time in my hands, partially because my phone internet wasn't working due to missing APNs (gone missing after three days of upgrade, and no new apps installed), and started looking into the logs.

Found some issues, don't know the exact extent of the problem, but let's go into them:

The /system/etc/init.d files run before the services are started, so the script S65priorities is trying to renice programs that aren't running yet, making it ineffective.

I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): USAGE: renice [[-r] priority pids ...] [-g pid]
I/run-parts( 1309): run-parts: /system/etc/init.d/S65priorities exited with code 1
I/logwrapper( 1309): /system/xbin/run-parts terminated by exit(1)

Since the run-parts was terminated, the script S99perfect isn't being executed, giving us one more ineffective. Maybe it should be run from another place, like rc.local, if the android boot follows the SYSV standard, this would be the last file to run.

I also found the culprit for the long delay on boot. The S20defrag script is searching for *.db on all filesystems and running a sqlite3 query to try and make the databases smaller, but it is taking a long time to run. Also, as far as my tests went, this is the culprit for the APN issue, since I got my APNs and the ultra-fast boot back when I removed this script from execution.

I/run-parts( 1298): Defragging /data...
I/run-parts( 1298): [B][COLOR="Red"]Wed Feb 29 01:58:41 BRT 2012[/COLOR][/B]
I/run-parts( 1298): Error: no such collation sequence: UNICODE
I/run-parts( 1298): Error: no such collation sequence: UNICODE
I/run-parts( 1298): Error: no such collation sequence: PHONEBOOK
I/run-parts( 1298): Error: no such collation sequence: PHONEBOOK
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): Error: database disk image is malformed
I/run-parts( 1298): /data defragged successfully.
I/run-parts( 1298): Defragging /sdcard...
I/run-parts( 1298): Wed Feb 29 01:59:25 BRT 2012
I/run-parts( 1298): /sdcard defragged successfully.
I/run-parts( 1298): Defragging /emmc...
I/run-parts( 1298): Wed Feb 29 01:59:25 BRT 2012
I/run-parts( 1298): /emmc defragged successfully.
I/run-parts( 1298): [B][COLOR="red"]Wed Feb 29 01:59:25 BRT 2012[/COLOR][/B]

It took almost 50 seconds just to "defrag", and I hadn't change nothing in three consecutive reboots. And it also have some errors being reported, I didn't got into details as to fine search for the errors, and will disable this script from my phone.

And found some problems with your sysctl.conf file, it has windows line brakers:

vm.swappiness = 0^M
vm.drop_caches = 0^M
vm.page-cluster = 3^M
vm.laptop_mode = 0^M
vm.dirty_expire_centisecs = 3000^M
vm.dirty_writeback_centisecs = 500^M
vm.dirty_background_ratio = 65^M
vm.dirty_ratio = 80^M
vm.vfs_cache_pressure = 1^M
vm.overcommit_memory = 1^M
vm.oom_kill_allocating_task = 0^M
vm.panic_on_oom = 0^M
kernel.sched_min_granularity_ns = 200000^M
kernel.sched_latency_ns = 400000^M
kernel.sched_wakeup_granularity_ns = 100000^M
kernel.panic_on_oops = 1^M
kernel.panic = 0^M
kernel.hung_task_timeout_secs = 30^M
kernel.threads-max = 5000^M
kernel.sched_child_runs_first = 1^M
kernel.sem = 500 512000 100 2048^M
kernel.shmmax = 268435456^M
kernel.msgmni = 1024^M

Linux can't understand those line brakers, and may sometimes interpret them as part of the line, generating errors.

And, if it isn't ask too much, would it be possible for you to add the bash shell from (here) into Neutrino? It's a way better shell to work with, specially when you are working with scripts.

I will keep looking for something more... since I'm with my old friend insomnia... ;)