1) They do stack. I'm semi-sure, though, that the returns are diminishing. A 1 ton HA 4 is going to give you more benefit than four .5 ton MA 1s. The machine will eventually reach a point where pretty much regardless of how high class a MA you stick into it, you'll still get a MR/TR penalty from installing the MA.
2) You'd have to code-dive to get the exact numbers, which is something I haven't done, but the source is open.
3) Can't remember what the + actuators are. There's only one sort of actuator as far as the engine's concerned, though. Everything else is the particular item, which can have adjusted price, weight, and toughness (at least for HAs; some of the other things, weapons particularly, have more things you can muck with.). Sounds like the plus ones have been lightened. There are no emergent benefits to higher class items, just improved ones it previously had.
