As far as measuring voltage at the MPEM, I believe on that ski the MPEM is grounded directly to the engine block but it's not clear from the schematic, the ground for the MPEM could be inside the e-box where the ignition coils live.
While on the subject, the e-box ground post is a known trouble spot, there is on most seadoos of a certain vintage a post inside the e-box where several grounds are all tied together but get this, that post is made of plastic and there is a screw threaded into this plastic post that over time is known to loosen and allow high resistance for these grounds. That would be the grounds for starter solenoid, both coils, and at least another ring terminal connector going to the engine block and maybe one for the MPEM.
So take a close look at that grounding post in the e-box, the fix for it is to drill a hole through the bottom of the box and put a threaded bolt through with a nut/lock washer on the bottom side, preferably all stainless steel.
So, if you want to measure the voltage directly at the MPEM while cranking, you should first determine which ground feeds it (connector 3 pin 25) and the power itself is on the 5A fuse, so use those test points. You can probe the fuse itself, there is an opening at the top corner of the fuse that's accessable with the fuse installed, look carefully and you'll see the opening there, there are two of them to allow for in-circuit testing.
I'm really not sure how much current you're liable to see with the clamp meter while cranking, it's liable to be quite a bit, so I'm interested in what you find out.
As far as gaping the plugs goes, if the gap is too small then wet fuel can bridge the gap and short out the plug. Our engines run rather rich (2-strokes do this) so it's unnecessary to have a big fat spark to ignite a lean mixture. Our combustion chambers are rather densely packed with a fuel charge under compression so the challenge mostly is to have a small enough gap to successfully force the spark to jump the gap. It can take quite a bit of voltage to force the spark to occur.
So if you make the gap too large you might get no spark (missing) under certain conditions that are harder to fire (such as WOT), or if the gap is too small the fuel bridges the gap and shorts the plug (fuel fouling).
I shoot for 20 thou, under the premise that as the plug wears the gap will open up. Also, a narrow gap is less likely to misfire due to lack of spark but is more easily fuel fouled so if one of my carbs goes pig rich for some reason I expect the fuel will short the plug and I can find a problem early, that way.. But I know what the motor should sound like anyway, so might be a moot point.
I think if you gap the plugs right to the middle of spec you're good to go, two different guys can gap a plug differently depending on his gauge, either a flat feeler or wire. Wire gauges are the best way to go, IMO.
The new fuel regulator holding pressure might help depending on what the previous running pressure was. Since running pressure is what really counts then, if the running pressure hasn't changed then the performance isn't likely to change.
It's just that one way to test a regulator is to examine decay, something like 30 secs or less is likely a bad regulator that has trash like dirt. leaves, or corrosion on the valving surfaces or some other type of corrosion/dirt jamming the works, or it could simply be worn out. Just b/c a regulator holds pressure doesn't mean it's working, what counts is the regulator holds the pressure at some predictable value while the engine uses fuel from the fuel rail. If the regulator was leaking off fast then I'd have to think the pressure would be too low during cruising or WOT, and the engine might run lean enough to roast a piston or misfire.