I am using a gen 3 TB on my gen 2 MS setup, they are identical in how they work, just follow my instructions for the idle up valve and you are good to go. The TPS is extremely easy to calibrate- open it, press calibrate, close it, press calibrate. No problems there.
No one can or would want to use the AFM with megasquirt. MS comes with an internal MAP sensor anyway so pull your stock one out and sell it for a crazy high price for someone wanting a gen 3 electronics swap. We all ditched our AFM as soon as we could.
Chances are your ignition system will not work or will be much to complicated just like the previous generations but no harm in trying... follow the instructions for general dizzy setup in the megamanual. Previous gens have trouble with noise filtering which is why no one has got MS to work with the stock system. I recently changed my dizzy cap on my gen 3 mr2. I did notice that the pick ups look a little different so you might be in luck. Otherwise get EDIS or coil on plug and be done with it- very easy.
IC pump??? you can set this up using a spare output pin, you can run it using any criteria you want, it can come on at a certain rpm/boost/coolant temp or any combination of anything you can think of.
What MS and board are you running and with what code? Hope this helps, otherwise flick through all 217 posts in the FAQ and hopefully most questions should be answered.