I've read your post several times and it's difficult to understand what you are asking. When you ask "how do you make new modules?" are you talking about creating modules not available in the basic game, by modding?

In the basic game there is no way I know of to create a new module beyond those that show up automatically on the Shipyard screen as you gain techs, if that is what you are asking.

So, what you're saying is that you figured it all out by yourself, right?

Although, i think you may be in for a ride if you wish to ADD functionality to extra-custom modules - properly detected by code, ready to fitted on hulls, providing specific features, etc.

I know that modifying Troop quantities is somehow as easy as changing the data field value, but giving them OTHER assets would involve in-code bit swappings and patchy stuff which may render the game flawed and even, crash it.
Believe me, i tried... and i decided to stick to actual gameplay principles when it came to simply add a few modules to the current short list of five defaults.

Images, UV-Mapping or 3d modeling is a different issue - which takes more patience rather than fiddling with module(s) functionality.

Which is also why, the X-Com/Aliens ships will be designed using the genuine valid isometric frameworks (OF and FROM real map.dat files, original and visually very similar, including a slight tilt of the front perspective to show floorplans and all components aboard the ships.) while taking advantage of the Hard-Points variable conditions.
Knowing the GC engine doesn't allow on-map viewing of the ship 'underneaths', it would have been awfully stupid to use the UFOD Power-Source gizmos as Engines, slap it on the floor plans smack middle, and not be aware of the actual proper propulsion device true location (even if at the right angle!) without spinning the ship itself to the back perspective.
Just the Alien Battleships/Dreadnaughts have FOUR engines on the first layer from a set of FOUR... each with a specific floor plan.
Complex, but quite possible- if not i'll simply use a general Flooring grid layed out on the last available level.

So, a small Scout would look something this;

........../-\..........
......../-----\........
....../--------N\......
..../------E------\....
.....\L----------/.....
.......\-------/.......
.........\---/.........
..........\W/..........

(E)ngine
(N)avigation array
(L)ife Support module
(W)eapon

With Hulls receiving some Defense "paneling" stuff.

!!! Instead of a flat boring square box.
Now, comes the fun part -- Animations!
The real UFOD & TFTD ships DO have full tilesets of animated components.


- Zyxpsilon.

You must not be verygood at 3d modeling because all you need to do convert a engin model to X create a tech for it thats it and besides and the X3GC2 mod I saw that it is possible to make new parts and modules so I tried it and they showed up.Its not hardcoded so it should be easy to create new parts.