Interesting issues when swapping parts (1999 GTX Limited)

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Ryan727

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Hey guys, new to the PWC world. So I recently purchased two Sea-Doo GTX's. One is almost ready for the water, the other needs a new top end. The almost-water-ready one was converted to premix, the other is still on the pump. The almost-water-ready one is kicking at 150 PSI in both cylinders.

Anyways, so I'm working on almost-water-ready one and ran into some more issues (of course, right?). Upon trying to give it a start after rebuilding the carbs, I have no spark in the PTO cylinder. So my first thought is to go grab the whatchamacallit (whatever is on the other end of the plug cables in the electrical box) from the dead ski, and swap it over. So then I realize they are different (i'll post some pics).

Not firing PTO electrical box (only has one thing where both plug wires go into):
IMG_20180623_194650.jpg


The one I swapped into the ski (you see it has two things, one for each plug wire):
IMG_20180623_194703.jpg


The only piece not swapped was the second positive cable. Not the one that goes to the battery, but the other one that comes off the solenoid and goes towards the front of the ski.

So, after swapping them, I get absolutely nothing to the starter. I'm getting juice, because my ski is beeping when the lanyard is put in (two beeps). But when I go to fire it up, it doesn't make a chirp - no ticking or anything. So I thought maybe it was the solenoid, so I swapped the one I knew worked (from the first picture) into the second electrical box, and still get nothing. Both 15A fuses are good in either box.

So, before you add some thoughts, let me add a few more things unrelated to this particular issue, but I find odd:

1. Both are 1999 models, but have different electrical boxes. Wondering if the second picture was a replacement as it looks brand new.

2. They both also have different MPEMS (I have pics if needed). Could this be that the box I swapped isn't compatible with the MPEM?

3. Once I insert the lanyard, I get the normal two beeps. Then, no more than 15 seconds later, I get one long beep. Didn't see anything related to this on the shop manual. Is that the ski just telling me, "hey we're shutting down, you may have forgot to take the key out."?
 
Update:

Upon further viewing of the harnesses, there appears to be one more wire in the box harness then there is on my harness that plugs in to it. This additional wire is for the second coil pack for the spark plug wires. I do see the additional wire on the harness still in the ski I pulled the box from. If I swap them, could that resolve the issue? Or will that harness even be recognized by my MPEM?
 
single coil set up is used on 98 model - dual coil is 99 they also use different 'mag cups'
 
Almost wondering if the entire inside of the ski was swapped with a '98 951. MPEM looks to be 1998 model as well (harness inputs arranged in more of a square than horizontal at the bottom).. Both ski HINs end in "999", just different insides.
 
I'm going to first trim my plug wire back a quarter inch and see if that's the easier fix here. If that doesn't work, I'm going to assume the two boxes I have are not interchangeable?
 
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