So I played with the 1.0.9 server zip that Lartza linked.
Fixes:
Tin and copper dusts smelt correctly. This is nice considering they added the ability to split copper and tin ore into 2 dusts but the dusts were never made smeltable.
MFFS stuff seems to be working. I heard quite a few complaints about them not working but I never noticed it. They do work now as far as I can tell. The extractor seems like it's slower now. Not sure if that is a bug.
Bugs:
The uranium-radioactive waste id confusion is still present. This is still a game breaker bug for me because without starting a fresh world, all uranium already present is now deadly and useless. It is possible to go into the AtomicScience.cfg file and swap their ids but every client has to do that also.
Any Mekanism generator item you have in your inventory or chests seems to be turned into a Null Render item. The items are still in the game but something must have been done with the ids and they resorted to Null Render. Possibly fixable using the above method but once again, every client has to do it.
The item id confusion completely ruins the server for anyone who is just updating a world to a newer build. At this point I'm sure they're going to screw people either way with a fix. Either people with old worlds will have to abandon their current worlds and start fresh, or people who have started after the 1.0.8 update will have to abandon theirs when the change is applied.