Yeah, it seems the various attacks do cause different damage:
Front laser: 1 full bar
Contact with boss (anywhere) 1/2 bar
Ground dust attack: 1/2 bar
Rear shell attack: 1/2 bar
The best news is I have worked out a way to hit with every single frame on the first Rolling Thunder. What's more interesting is that I've actually discovered that Dragon Frye's Fireballs actually do damage over time if they are fired close. It seems they cause 500 damage/frame, and the most I've managed to get so far is 7 frames of damage. I'll keep working on it to see if I can increase DF's damage even further.
EDIT:
Stage 5:
http://www.youtube.com/watch?v=a1Chvy3nUT8
Only thing I need to fix here is not getting the Potion at the end of the first part of the stage. Otherwise, this is pretty much as fast as possible for this Stage. A lot of side-trekking for items, but they all play an important part in finishing this stage quickly, mainly for the boss. The invincibility fairy makes getting through the middle part of 5-2 easier, although it does work out a bit slower overall it means I can get through there without taking damage.
EDIT:
Time for an update!
First things first, I am completely ignoring the invincibility fairy. I never liked the idea of picking it up, because it does waste time over the stage, but it saves 1 and a half health bars. (1 by going through a flame jet that cannot be leaped over, and half by jumping into the giant mole creature near the steam jet that cannot be killed fast enough).
I have refined the first half of the stage along the long corridor gauntlet, saving another 1/2 health bar and 19 frames total over the first half of the level.
Further improvements came from jumping over or through most of the flame jets in the second half of the level, avoiding the invincibility fairy (wastes far more time than it would save), and improving the boss further.
On the subject of the Boss, I have removed Thunder Raven's appearance completely, (+900 damage is not worth the frames wasted bringing her in) and optimised the damage taken and dealt even further, by carefully positioning Dragon Frye in the most optimal places for his fireballs. It seems 8 frames is the most you can get, and at 1500 damage per frame maximum, this leaves a possibility of 12,000, close to a quarter of the boss's HP alone. Maximum damage isn't always possible because the positioning has to be frame perfect, but I do get Dragon Frye to contribute damage 3 times in total, the main damage coming from Alisia's Rolling Thunder's, each adding just over 19,000 damage. This makes the boss's HP of just over 52,000 seem pretty pathetic in comparison, even though he has the second highest HP of the bosses in this game, and in a normal game would take several passes to finish off. I have even finished the boss with more health left again, so I can avoid getting another potion (I chose to get the one near the area with the third Thunder Level Up this time, but that can be easily removed).
I'll post another WIP once the potion situation is fixed, and that will have completely optimised this Stage finally! After that, it is onto the fun little maze of Stage 6!