When starting "All the Mods" version 0.0.0.9 from Curse with Bookshelf 1.9.4-1.2.1.251 loaded, JEI failes to start. As per your post for issue #34 the most recent version of JEI is being used.
This is the crash report generated: http://pastebin.com/t3Lp3aNw

If version 250 of Bookshelf is used, The world loads with no issues. It would appear that there is a bug within the most recent release of Bookshelf causing a crash against the most recent release of JEI.

Yes, a new update for DarkUtilieis is in the work. I have also been forgetting to set the minimum Bookshelf version in the DarkUtilities file. Fix is already done on my local copy.

This is fixed in latest build of Dark Utilities. 95a2b095acb393f7d75518e2a6cd9792996be8ec

Looks like the latest version of JEI isn't updated to the latest version of Bookshelf. You have to downgrade Bookshelf for Minecraft to work.

Downgrading to a previous version of JEI is not possible as the previous version is compiled against 1.9.0 which will not work with the changes in forge that occurred at 1.9.4.

I am linking/cross posting this thread to the JEI github so that they can work to resolve the issue.

It's the JEI module 'moreoverlays' causing the crash, not JEI itself.

JEI and MoveOverlays have nothing to do with it.
The crash is very clear here:

Caused by: java.lang.NoClassDefFoundError: net/darkhax/bookshelf/lib/util/Utilities
    at net.darkhax.darkutils.items.ItemBlockCake.func_77624_a(ItemBlockCake.java:36)

DarkUtilties requires a different Bookshelf from what Gunner has. Here is the proof:
https://github.com/Darkhax-Minecraft/Dark-Utilities/blob/master/build.gradle#L67

Rofl, I can't read crash logs. Sorry.