I figured I would add my experience here, in case it helps someone figure out how to get everything working again...
I downloaded the new mod manager last night (0.50) and tried to run the game after merging all of my mods. I could get to BE, but when I tried to view the weapons or mirror or schematics, then clicked on anything (sell/a piece of equipment/etc) the game locked up. It didn't crash and I didn't get a black screen, it just locked up and I could do nothing. I had to ctrl-alt-del to get out of the game.
I tried again today to see if anything else would work. Going to the Frostback Basin caused the game to throw me out. No black screen, no lockup, it just booted me out and the game stopped running. I checked the running processes and it was no longer there. I managed not to throw my laptop across the room and decided to test a bit more...
Using the newer mod manager (0.51), I did another merge, leaving all of my mods enabled. The game started, i could travel to Frostback Basin with no trouble whatsoever, interact with the environment. bathe in the poison spider blood, and everything was dandy. Encouraged, I traveled directly to BE. Again, I made it there with no problem, but again, any time I open anything - mirror, weapons, schematics, materials (I reloaded and tried each one) - then click on anything, the game immediately locks up and I have to ctrl-alt-del to kill it.
One more addition: I use LL Skyhold Clothing (as well as every other LL mod in existence) and it no longer works. The game loads, as I said, but the Skyhold clothing is back to that ugly ass tan pajama getup instead of the nice red and black clothing from LL. Other recoloring works fine. I used the tinter mod in the basement at Skyhold and it works fine and the recolors stick. It's just the stupid pajamas that are back to being tan.
I haven't checked all mods, but most others seem to be working fine, including Black and White Skyhold, no waiting for war table missions, gothic font, and war table more materials (seriously, wtf was Bioware thinking having scouts sent out to collect materials and coming back with three lousy herbs??). I may test more later, if I have time. If this is helpful to anyone in the modding community, please let me know. If not, I'll keep it to myself! 