Score updated on first page. I've determined that beating all 3 loops without dying is inconsequential compared to hitting as many enemies as possible with the score glitch we discovered. Plus, of course, getting all of the hidden bonuses. These include, but are not necessarily limited to...
Stage 1: Arms (up to 4k each), Bombs (up to 120 each, not worth the risk), Boss (20k)
Stage 2: Boss (20k)
Stage 3: Dragons (2k each, possibly more), Boss (20k)
Stage 4: Pods (2k each, possibly more), Tendril pods (2k each, very risky), Boss (20k)
Stage 5: Gradius (2k each, x3), Boss (20k possible, confirmed in emulator, extremely risky and probably not worth going into stage 6 gimped for it)
Stage 6: Moai Heads (2k), Snake (10k), Heart (30k!)
The above are my observations. I may be a bit off on a few counts, especially on the harder enemies. Some of these numbers are from Guts, who has also been checking on scores with me.
My first loop I landed just over 380k with no deaths. Second loop I shat the proverbial bed on stage 6, and thus missed out on the huge score bonus from the heart. 3rd loop went incredibly well, aside from a few more deaths, and one last "fuck you" death in the final escape.
Overall a good run, though it may yet be improved upon if someone is incredibly skilled at hitting the glitch on the enemies I posted above, and doesn't fuck up the few places I did. I'd estimate an almost perfect run with all of the main glitch kills (bosses particularly) netting you a 400k loop 1.
A TAS run, if someone were so inclined to make one, I would probably estimate should come out to around 450k; this would include double points on all bosses and all major enemies (and is purely an estimate based on experience and some simple math).