ValoWay, that is quite a mod list! I can't recall ever seeing one as extensive for SH3, especially on top of a megamod like GWX. First of all: Are you really sure you prefer all those mods. Have you actually played the basic SH3-GWX game and then added mods to it? Because GWX is pretty good to start with. You might decide you don't need all the other mods. And more mods = more opportunities for mod conflicts, which is what you are seeing.
Second item: The instructions for GWX tell you to activate any and all of the GWX add-on mods immediately on the basic SH3-GWX. Again, try the game without them first, then add on the add-ons (
).
Third, the instructions for h.sie's patcher (These instructions are included in GWX Hardcode Fixes, and apply to that mod also!) state that the assembled mod package for h.sie's patches should be activated LAST. There is a very good reason why this instruction should be heeded! The only mod that you should ever activate AFTER h.sie's patcher mod (what you call GWX Hardcoded Fixes) is an extension to h.sie's patcher created by Stiebler.
Fourth, GWX Hardcoded Fixes is a specific instance of h.sie's patcher intended to be used with the basic SH3-GWX ONLY! Most - but not all! - GWX add-on mods will not conflict. (Integrated Orders and Alternative Flotillas are two that WILL conflict.) So any mod you activate on top of basic SH3-GWX MAY cause cause problems with GWX Hardcoded Fixes.
Finally, ANY GUI mod that you activate (such as OLC Gold Mk II) WILL conflict with GWX Hardcoded Fixes. It doesn't matter whether you activate the GUI before or after GWX Hardcoded Fixes. Things will not work properly.
So my advice is, peel off all those mods, down to basic SH3-GWX. Try the game that way. Then add GWX Hardcoded Fixes ONLY, and try that. h.sie's patches add a lot of goodies I think you may want. DO read the documentation so you know how things are going to work once this mod is installed. THEN, and ONLY then, you can add other mods. Remember to activate GWX add-on mods first. Remember to activate GWX Hardcoded Fixes LAST ALWAYS. If JSGME tells you that a mod wants to overwrite part of another mod, DON'T USE IT. If JSGME tells you that GWX Hardcoded Fixes is going to overwrite any previously-activated mod, remove the previously activated mod and DON'T USE IT. When you add mods, always add just one mod (with GWX Hardcoded Fixes activated after that) and play the game enough to see what the new mod has changed, so you can make an informed decision whether to keep it or discard it. If, after adding a mod, you get strange game behavior, discard that mod.
There are people who will tell you that none of these restrictions is really necessary. They are correct. If you know enough about modding and the SH3 game files, you can work around any of them. But until you feel comfortable making your own mods, you should probably stick with these rules. Try my suggestions and you should be able to play and enjoy the game pretty quickly.
Just one more thing: Most mods are not written to be compatible with most other mods. This is especially true with the megamods, like GWX, LSH, and NYGM. If a mod's documentation SAYS it IS compatible with another specific mod, then it is. If it does not say so, don't assume that it is. It may be compatible, or it may not be, but it was not intended to be compatible by the guy who made it. If it were, he would have said so.