I've done no changes to any weapons themselves, but it's slated for the total conversion mod. I just wanted to get out what I had finished since I promised it would be out this week and I'm not sure how long it will take to rig up some new TIE Fighter equipment. I'll likely post an update that includes just those changes to the TIE Fighters. I'm still debating between making the TIEs extremely weak (both defensively and offensively and having about 6 to 12 launch at once) or keeping it roughly the way it is now (except change the graphics/audio of the weapon and reduce its damage maybe). I mainly just picked that weapon because it was a green laser of sorts until a better one can be made.
As for the UI and the cargo, this is likely an issue of your resolution. At 1280x960, I don't have the problem. When making the ISD, I modeled it stat-wise largely from the Damocles. This includes the maximum cargo capacity of 20 items. So if you ever happened across the Damocles in an un-modded game, you would theoretically experience those same problems. I'm not familiar with them since I don't use a low resolution. What size do you use?
Regarding the ship being overpowered, it is definitely overpowered when you've got it all rigged up with the best equipment and especially on the easier gameplay settings. I only play on the hardest settings and the largest map. Despite its strengths, it is not remotely invincible. Many a time, I've lost battles to the Tan Ru. I've yet to fight the kwangi, but I suspect you're right about it losing to them without a fleet to back it up.
Ultimately, I want to set up purchasable items at Coruscant that adds a ship to your fleet. When that's implemented in the total conversion (if it's doable), I will likely reduce the strength of the ships to try and balance it out. I just think it'd be really cool to see 3 ISDs taking on a big fleet of bad guys.
Thanks for the feedback!