OKAY SO AFTER TONS OF FIGHTING WITH THIS PROGRAM, I FINALLY FIGURED IT OUT
(Sorry for the caps. I was very frustrated. OpenToonz crashed on me many times.)
So first thing: I completely edited my animation frames so that their resolution would match my output settings. 1280x720 pixels, 64DPI.
Next: Cleanup settings. I didn't know about this part, and spent hours figuring it out. Apparently, you have to change your cleanup settings from "Grayscale" to "Colors." And then you have to add the colors that you want preserved (in my case, Blue and red.)
Then: Actual cleanup (preview highly recommended) will convert the frames to a Toonz Raster File with the Cleanup settings specified.
LAST: "Convert to Vectors" I finally got it to work. Good Lord.

Not gonna lie, now I'm not sure if the anti-aliasing thing is valid, but I'll test that another time and post the results here if/when I do.