I may actually cry a little. I'm glad you got TMNT working.
Here's how I do my labels. It took me dozens of attempts to work out this method. You may consider it. I've actually reprinted and replaced a bunch of mine.
First buy 100 full sheet mailing labels off the ebay for ~$15 and print six labels to a sheet:
(I like to use the leftover white space to make EPROM labels and also has a note in there about what sizes the SEGA/EA labels should be)
You can do this before or after the clearcoating, but peel the backing side and cut slits underneath where it rests on the labels. Keeps you from nicking them up trying to peel them later.
Tape it to the vertical side of a cardboard box. One misty coat so you don't make the ink run. Wait an hour, give it a second coat.
Then cut them out as straight as you can manage. Run a sharpie sideways along the sides. You can see I've done about half this edge in this photo:
Here's the whole side done:
Then when you slap it on the shell, you don't have a white leading edge:
I've got a multicolor set of sharpies, so I use red/blue/orange/whatever as most closely matches the art.
(and this is an extra Cave Story cartridge. who wants it?
)