Ah-ha! Some of your mods are incompatible with TMO v2.5, and some of them are unnecessary, since they are already in the mod. Start at the bottom of your list, and remove all of them up to the TMO v2.5 listing. In other words, all but the one. Then re-activate your Spyron, which will wipe-out your TMO CareerStart and the sub's associated with that. Empty the Save folder associated with this install, and run the game again. See if it functions correctly for you to run the Spyron mod. I am thinking that there were a few things that had to be changed in that, but I am remembering an old aanker post, and it might have just been his custom install.
Anyway, if everything seems to run OK, go through the ReadMe documentation of each of the other mods, to see if they are compatible. Some will say in the text documentation that they are for the Stock game only. Others will say like "for use with TMO v1.9" or some such. You'll have to decide what you want to keep and alter for use with TMO, or just leave out, if they are not compatible. Read through some of the early posts in "
[REL] Trigger Maru Overhauled", and you will occasionally find posts from folks inquiring whether "this mod or the other" would work in TMO. The answer was generally "No", unless it was specifically written for it. You might also ask other players what all they run with their TMO 2.5 mod. Another choice, if you want to alter TMO, is to use Bleiente's "
Ralles RealModPack for TMO_RSRDC_OTC", which is Bleiente's "mix" of TMO, RSRDC (Run Silent Run Deep Campaign), and CapnScurvy's OTC (Optical Targeting Correction) mods. The "key" is to keep the mod list as simple as you can, so you have less chance of something going wrong. My guess for your deck guns, is that something is partially overwriting your "Default Bow Deck Gun" mod from Sniper297. That is the type of mod that would generally be one of the last that you activate, but even still, if the "rooms" on the subs, or the "placeholders" for the gun do not match what the mod is writing, you will end up with no guns...
Do one step at a time, and test. If it works, do the next step, etc. You might also have to empty the Save folder between each test, depending upon what your new mod is over-writing. It can be a very frustrating process to go through.
