Before I install any other mods based on this guide: http://tesivpositive.animolious.com/?page=guides_mod_installation&subpage=complete_installation_guide&step=4
Not that familiar with Tomlong's guide but I'd definitely recommend focusing on the FCOM install before starting to add lots of other mods. If you like Tomlong's guide, follow it in conjunction with the opening post in http://www.gamesas.com/index.php?/topic/1160205-relz-fcom-convergence-and-ufcom/. Start from a clean install. Patch the game to 1.2.0416 if needed. Load a new game just to check that it seems to work. Install OOO, i.e. OOO 1.33 Complete patched to OOO 1.34 Beta 5, and load a new game again just to check that it seems to work OK. Then focus on the core FCOM install and start a new game after finishing it - now doing the starting dungeon and beyond so you'll notice if there are any issues.
After that, add one or a couple of mods at a time while checking for issues/stability. You can do this while playing - in fact, it's often best as you can check it out as you go then. One upside with having a core FCOM install that's stable is that you can fall back on it if something happens. The same for adding just a couple of mods at a time - if something gets messed up it's easy to fall back. That is if you save a lot - which is recommended.
The most common mistake is probably missing resources causing missing meshes/textures in game or even CTDs. So make sure MMM.bsa is renamed to FCOM_Convergence_Mart's Monster Mod.bsa etc.