I scored 55 million yesterday and that was with only completing 4 missions. The key to scoring is to hit the combo's. Most of my points came in during Vengence MB and Klingon MB.

This.
KM mb scoring is based on how well you do in the level 1 missions. Combos in KM mb will help with scoring as well.

I believe 3-in-a-row scoring is based on how well you did with its relative missions as well. Can anyone confirm that?

Correct. I don't know the exact math/logic behind it, but your ramp/spinner/pops value varies, and I get base ramp values around 1M when I play the 3 right-side modes well, and around 600K base when played poorly.

Play the 3 right-side modes well. Get your alternating ramp combo shots going for around 20M in value during Super Ramps. Profit.

Yeah, forget the sofware changes and focus on combos and completing modes, and then combos again during KM MB to really cash in on your mode scores. Have you watched Bowen's tutorial video? If not I highly recommend at least the first half.

There is no magic adjustment to make scoring rules different. If you want to make the game easier so that you can see more of the game, you can try:
1. Go to the INSTALLS menu and select extra easy.
2. Go to the INSTALLS menu and select add-a-ball so that you get extra balls instead of replays.
3. Change replay levels to 4 instead of 1. With add-a-ball, this gives you 4 chances of extra balls
4. Move the out lane posts to the lowest position.
5. Change "coil pulse power" to soft.