What were some of those error messages? That would help in figuring this out.
What were the circumstances of your "install"? Since the odds of having a "clean" game after having used other mods are rather small, it's best if you start with a clean install of the game. Not absolutely necessary usually, but... You should delete (or backup and move) the "My Documents / SH4" folder, which is the old save folder, prior to installing the game again. Take a snapshot with JSGME before you begin with the modding. Then be careful of the folder structure, and enable the mod. The use of
LAA or similar is recommended, due to the memory footprint (see also
Windows10; Large Address Aware; SH4 Install). The modded game should load faster than stock, and you should NOT get any error messages. The only thing that takes a while to load is the Museum, and that is just due to the amount of "assets" used in the game. This "beta" version of the mod is more well-behaved than a lot of the "release" versions of other mods. That's a testament to the skill of the modders on this team (I would name CapnScurvy, cdrsubron7 and s7rikeback directly, but I'm afraid I'd embarrass them - tic). If I was a betting man, I'd say there was either an issue with "cross-contamination" from a previous mod, or you have a bad folder structure in the MODS folder. Not 100% guaranteed, but close to it.
About the only other thing that would mess you up is computer specs. Take the stock games recommendations, and double them, so you ~need~ a dual-core with at least 4gig of RAM, and a strong graphics card. The latest / greatest is not needed, but you definitely want strong computer gear that is about 5-6 years old or newer. Though it does run on my 2.0g intel core2 duo E4400 and 2 gig of RAM, with an nVidia 6200 AGP vid card with the graphics all set low, the frame rate will dip below 20 fps quite often, so I use it as a test bed for loading, and not much else (the ME). But when I'm playing, I'm on a similar computer that has a core2 quad running at 2.4, 8gig of RAM, and an older PCIe card with more memory, but I'm at a much higher graphics setting (not full-on). Nary a hitch...
Get us those error messages...