Normal (v0.22)
S20-TBL - Lise - 128,682,360 - 4
I practiced a bit more with Lise, and found I could more than match my Francette score for stage 1 (in the run above, though, accidentally died during Fram A., which cost me 1 mil).
I found something out: If you let your Counter run out normally, some of your opponents will be shooting silver jewels at you instead of bullets for slightly more than one full second. Great for those large machines in the vertical section of Stage 2.

Also noticed that you can gain score by beaming enemies that are about to spawn from the top of the screen. The game basically thinks your beam is hitting them, but won't actually register damage until they fully appear onscreen.
Aru-san: Awesome replay, I usually just let 'er rip at 5K Counter during the pre-midboss section. Didn't know you could spawn a lot more enemies if you wait until you get 10K and are nearing the midboss. Great technique.

EDIT: Tried your Counter timing, couldn't get it all down pat yet but I managed to hit 34,361,670. Thanks.

EDIT 2: I recently got 45,454,220 on Stage 1 with Lise using a variation of your technique. Here's the replay file (need to rename it for the game to play it).