[Coffee or Lard?!]

Hi, my name is Mike and I have playing SH4 for over 1 year now. I recently had to have my computer redone because I had some viruses. Before I had it redone, all of the mods that I had installed worked just fine. Now however, none of them work. Everything from my hard drive was transferred to an external HD before my computer was redone, and transferred back when the work was finished. I reinstalled SH4, updated it to v1.4 with the patch I had downloaded, which for some reason is the only SH4 download I have that still works, and then reinstalled the mods as I had done in the past. The problem is that none of them worked. I tried manual instillation, the Generic Mod Enabler, and even re-downloading two of the mods, and nothing works. Is there anything that I can do to fix/correct this problem? If so, please let me know ASAP. Thanks!