As soon as I start Fallout 3 I get the Stop running message. I tried redownloading and installing from Steam but that did'nt work. The problem might be because I had the Nexus mod manager and the Fallout mod manager at the same time before deletion.

Edit: I verifed my game cache and now Im downloading a couple hundred files I'll see if that helps.

I have both of them myself, and my game runs fine. I'd use the Fallout mod manager over the Nexus mod manager, though - FOMM seems to do a better job handling Fallout 3 FOMOD packages.

Your problem is more likely some sort of mod issue, such as using conflicting mods or having the load order incorrect. Throwing hundreds of files at the game at once and then hoping for the best is not recommended.