I can help you with #4 as I just fixed this issue! It is correct that the MegaSquirt injector driver wasn't really made to handle 6 injectors -- it creates too much electrical noise for the MegaSquirt to handle. HOWEVER, before you go out and buy resistors to put in your system, there is an easier way! It is very simple to fix the MegaSquirt injector drivers to allow them to handle 6 low impedance injectors with ease, and it ends up getting less noise than installing resistor packs inline with the injectors! Run down to Radio Shack, and buy yourself a 47uf 35V capacitor. Now, take the case off of your MegaSquirt, and find the "boot" header on it. On the underside of the board, it should have the back side of the "boot" header pins sticking through. Solder your two 47uf 35V capacitor leads to the two "boot" header pins. Stick the case back on your MS, and bam! You're ready to go with your new, low noise setup. This may fix other problems you are having as well. For me, I had trouble getting the engine to rev over ~5k or so without having it cut out, and it would also cut out randomly while cruising. Both issues are completely gone.
Edit: I also know 5, it should be 2 per cycle, alternating