I created a custom IPSW using PwnageTool 4.0 and Restored with it no issue. But, iBooks was not functional (known issue).
I created a custom IPSW using PwnageTool 4.01 (supposedly fixed iBooks) and Restored with it, again no issue. But, mobileconfig files are not recognized, which makes it difficult to adjust your APN, for example.
I created a second IPSW with PT 4.01 and Restored and still see the same issue. I then Restored with an IPSW from PT 4.0 and mobileconfig is fine. (But again, iBooks is not functional.)
I did the same pwnagetool 4.0, then went to 4.01. Even on the latest 4.01 I still can not get ibooks to work. The pooh book is not on the phone, if I try and dl a free book it get's to about 99% and just hangs. I exit ibooks and everything disappears. Tried searching google abou the issues and can't seem to find an answer. Just that 4.01 fixes the ibooks issues. Not in my case.
If anyone has a suggestion let me know. Other than that so far I have had no other issues.
My previous JB was 3.12 Blckra1n. I never went to 3.13 since it was not worth the trouble.
If I figuer out what the issues is, or a work around I will post it up.