I guess the ships that use the newer weapons can't be used because of the custom weapons.
I think that's something i will request for Megamek. Recognizing custom weapons, since it's a thing. HMA files should be you drop in there and it works.
First off gotta say...Love the new art and fluff nice job!
For new weapons we would need to add them to the base code. Truthfully we try an avoid adding custom weapons and equipment since it requires support to maintain them. They also often generate bug reports and player questions we aren't able to easily answer.
What about making versions with canon weapons? If they had canon weapons I would be more than happy to work up the MegaMek files for them and include them in the releases. Heck with your permission I would even include the art and link them as well.
I should also add we are working on a Large Craft editor. Currently its in the beta stages for Small craft and Dropships. JS/WS/SS support will be added over the next few months.