Interesting reading. I would be extra careful with spraypaints if that's the road you go down. Airbrushing an acrilyc just might be the better option, after having read this document.
As for lettering, I was thinking of using stencils to paint them on. Seems too intricate for decals or cutting...
Stencils certainly could work. But I would give one more push for dry transfer lettering. Most any model railroad supply store will have these and there is a military font which looks pretty passable for the Star Fleet lettering. The advantage to these is that the edges will all be quite crisp, where I'm afraid that stenciling might end up being too fiddly. It's certainly worth experimenting.
But the stripe and arrowhead (and maybe a ship on the back) will definitely be decals. Do you know any companies that print good, thick, decals? I've googled a few but am not sold on any yet.
There are a number of guys who do aftermarket decals for Trek
kits. Most all of them are willing to talk custom work, but I don't dare guess what they'll ask for it. The only two I've personally any experience with are PNT and JT Graphics. Both make very nice decals. I'm not sure how strongly I can recommend them, though... I've had customer service issues with PNT in years past and the JT Graphics stuff I've only ever got through a third party, so, I'm not sure what he's like to deal with personally. You can Google them. Seems like JT Graphic's site is undergoing some revamping, but I bet you can still contact him through it.
were in your shoes, I'd print my own. The pros use ALPS printers, which are very nice, but just get some Testors decal paper and run them through your inkjet printer. One quick lacquer spray seals them against water. If you can make that sample image in post #5, you should have no problem whipping up some fair quality decals yourself.
Again... It's worth experimentation.
Good luck with this! I can't wait to see what you come up with!