Ok, I'll uninstall everything through steam, go back to delete the folders for mods and scripts manually (yes, I did delete the folder manually before installing before) and try again. I have the 0.99.4 main downloaded in the 3 parts from the front page, though I admit I did not check the md5, I'll have to do that. In fact screw it I'll re-download just to be sure. And after installing that I installed the 0.99.45 update.
I will say for the part downloads, the mega links for part 2 and part 3 don't seem to work on my end. It tells me the file is no longer available. Initialy I got part 1 from mega and the other 2 from the alternate links, though I don't think that should be a problem.
EDIT: I do have the steam folder set-up on a different drive, not the system drive, I keep games on their own drive basically. But again, I doubt that should be an issue, I pointed the installers at the correct steam folder each time.