process of elimination, the easiest and cheapest thing to do is to check for voltage at the battery while riding and see what the voltage reads when acting up or not and then go from there.
also wouldn't be a bad idea to have a fuel pressure gauge hooked up while riding to see if anything out of the norm is happening. hopefully one of the 2 will tell the tale and we can move on. while you're at it make sure all the grounds are good. from battery to starter, from starter to mag cover and at the mag cover should be 2 ground wires from the harness.
may even check the resistance for the tps and air pressure sensor. the manual has the specs and which pins to probe on the amp 4 connector from the mpem. i heard that if the air pressure sensor gets wet with water it is ruined.
i am just listing the things that can be checked for free before you dump un needed money into it. keep us posted