I really think this run should be done on the SNES version.
If I recall correctly there is boss mode and a 100 round mode. (actually endless, but could be defined as ending at round 100). It's been a long time since I've played though.
Doing combos in vs (boss) mode can place horizontal or vertical rows of enemies on your opponents and lower the ceiling. You have to get completely crushed to lose, not quite like Tetris.
From GameFAQs - On the SNES game, highlight 'VS' and press Left + Start to access the hardest mode.
I think a SNES boss mode run on hardest mode would probably make the best run.
I also think the music is better on the SNES version. =p
EDIT: They might ruin the music in boss mode on the hardest difficulty. =/
Sample Gameplay in SNES boss mode.
http://www.youtube.com/watch?v=MSCP1NV3D70&feature=related
One more thing. Regardless of NES/SNES it seems to me like it would be strategic to pump the down button at specific frames while doing other actions, or in between actions in order to make bombs fall faster. This would surely speed up Bisqwit's WIP if it works. It may very well not work though.