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951 DI nightmare please help (no start)

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HumbleRestorer

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Bought a 2005 Sportster LE DI for a good price, but it has progressively snowballed into a total lemon which happens to be my luck.
History at the bottom of the post for more info

Currently I had the engine sorted (fuel pressure is good 27psi key on, air compressor pressure is good 80psi when cranking) and was battling an intermittent spark/weak spark issue that was preventing the engine from starting after it randomly shut off on me after 2 minutes of running

Come to find that the boat had taken on water inside at some point under previous owner, not flooded but enough to cause corrosion on most of the connectors, ground wires etc. I removed every trace of corrosion from connectors, ground wires, etc. I also replaced the ignition coils + their connectors (these were really bad) + checked all fuses.
Come to find that my initial weak spark/no spark problem came from the connector to the stator/trigger that was extremely corroded and almost burnt looking (engine was replaced by P.O. and shop did nothing about this connector). Seeing the state of this connector, I pulled the mag cover off to inspect inside and it was fine. Some signs of water but no rust and no corrosion or signs of burnt wires/connectors on the new engine/cover. Needless to say I ordered a used mag cover with low miles that came with a much nicer stator & pick up/trigger just to be safe. I double checked to make sure they had good or similar ohm readings as the one I took off and they did.

At this point now with the new mag cover installed whenever I crank the boat about every 10 seconds of cranking I will get a LOUD backfire out of the exhaust, that sounds like a gunshot. Pulled the plugs and had a lot of smoke coming from the MAG cylinder. The plugs are new but have definitely been fouled from all the diagnostic cranking + weak/no spark cranking I've been doing just to get the engine to this point the past couple of months.

Going to try some new plugs tomorrow as I searched and found a similar guy had this backfire problem and he fixed it with new plugs. I doubt I'm that lucky but my plugs definitely need to be changed regardless at this point.

Main question is, after having removed the mag cover and not touching the magneto cup, flywheel or anything else besides the cover, what could have possibly gone wrong to make it start backfiring all of a sudden when cranking? There were no issues found on the flywheel or mag cup when I inspected and no serious corrosion either.

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History:
I bought the boat in decent condition, it would start and idle but eventually shut down a few seconds later. Owner had put a new battery in the boat before he sold it to me that day. Enough attempts and it would stay running a little longer but eventually shut off again after a minute or two. On the drive home I stopped and filled it with fresh gas also.

Owner said it needed a tune up, took him for his word and bought new plugs + sent fuel and air injectors out to Florida Injector man to be cleaned and tested.
1 week later everything comes in and I install it, now the boat will not start at all, cranks fine.

For good measure I end up pulling out the fuel pump and replacing the internal filters + the external inline filter also from HFP

Also replaced air regulator with HFP version (no difference, but glad to report it works just as good as the oem one in case anyone was wondering)

Come to find out it was not starting due to low air compressor pressure. Had a leak from the air compressor line to the rave solenoid. Fixed that, still have pretty sub-par pressure at this point
Order diagnostic tools/fittings/gauge and replaced the rave solenoid with a new OEM unit + some other leaks in hoses. Also ended up replacing the entire air compressor with SBT kit for good measure. Engine now has good air pressure when cranking.

Got it to start and run again finally after running it on shop air bypassing the entire air pressure system for about 2 minutes (about the time it took me to go grab the hose and turn it on to see how long it would run on the hose) before it shut off on itself randomly maybe a few seconds after I connected the hose while the boat was running and it refused to start back up ever since.

Had a friend check for spark while I cranked since both air and fuel pressure were good when I re-checked them trying to figure out why it shut off and we didn't detect any spark on either cylinder when cranking (mind you this is maybe 20 minutes after the engine had just ran fine for 2 minutes at idle).

Proceed to check my ignition coil box and find the connectors in really bad shape, heavily corroded and the ground pin moves freely in the connector. Also found an aftermarket and a Chinese coil from previous owner. Replaced both ignition coils and connectors with this kit Ignition Coil Pack for 2000-2007 SeaDoo 951 DI 3D GTX LRV RX XP DI Sportster LE | eBay

Still would crank but not start with all pressures in good shape (fuel and air pressure). Looks like no spark still. Proceeded to clean the connectors behind the ignition box + to the mag housing. At this time I also went ahead and pulled the mag housing and the rest is above.

TL:DR Checklist:

Compression on both cylinders = 120 psi on both cylinders
Fuel Pressure is 27psi with key on 2 beeps
Air pressure is 80psi when cranking
New battery (previous owner)
New spark plugs (kinda fouled now)
New ignition coils + connectors
Low hours MAG Housing with stator and trigger/pick up
Corrosion on connector pins and ground wires cleaned
Measured resistance on plug wires and within spec/working
MAG Cup and Flywheel appear fine (no missing teeth etc.)
Air and Fuel injectors sent out to reputable place to be tested and cleaned
Has fresh gas
 
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Original state of the connector to mag housing before I cleaned it (I suspect this was my intermittent/no spark issue)1666574641184.png
Previous owner gave me the original engine (Old mag housing cover above, new engine cover below)
1666574650635.png

Mag housing cover I ordered off Ebay
1666574762418.png
 
Could you have the plug wires or coils swapped?
1666620771748.pngTop one goes to PTO, bottom one to MAG cylinder.
It's possible I may have switched the connectors to the coils around after the repair, I'll swap them and see if that changes anything. But I remember taking extra precaution to make sure I didn't mix them up.
 
Could you have the plug wires or coils swapped?
Just wanted to update, thank you so much for this comment, it made me double check and sure enough I had the connectors backwards. Swapped them over and no backfiring anymore.
I have good spark now on both cylinders, however the engine dies almost instantly after firing over. 12.2v static from the battery, 11v when cranking. Air pressure is good, fuel pressure I suspect is still good but will double check.

Any ideas what's causing the immediate stalling?
 
I see you stating "fuel pressure good" at 27 psi. There are also a lot of air pressure statements.
However, I don't see a fuel pressure reading while cranking. The 27 psi fuel pressure above the 0 psi air rail pressure is only the first step. The fuel pressure needs to be at least about 90 psi to even try to start, but preferably the full required 107 psi. The fuel pressure regulator makes the pressure 27 psi ABOVE the air pressure in the rail. So, can you verify the fuel pumps ability to keep that pressure difference even when the air rail is at the 80 psi?
 
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