300/440/550 550 backfiring through carb. VIDEO ATTACHED

This guy bought some parts from me(flush kit, throttle cable). Asked me if I could put them on and route the fuel lines for him and install primer. Ended up getting into it pretty far. Replaced the ebox, because his had cut wires held together with wirenuts, replaced start stop switch because of a no spark issue, he had no rev limiter and no restricters in the fuel lines so I put a known good limiter in. Got it running couldnt tune, ran like :):):):). Found cases had no sealer on them and seals were leaking. Tore the engine down replaced all seals and gaskets. Put it back together and it runs better, but pops thru the carb(was also popping before i tore apart). Its almost intermintent, sometimes it wont do it. Usually happens when giving a quick blip on the throttle. Im not sure if its a timing issue or carb. Ski is stock, flywheel has a 21 marked on it, head seems to be milled. This carb came off a ski that was running well a few months ago. I set timing at the static location. Heres a video maybe someone can guide me on what to do next. In my mind, im thinking advance timing and maybe rebuild carb. I want this thing out of my shop, way to much time invested for what Im getting paid(im and auto mechanic so jet skis are still new to me)
 
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It does it on the hose as well. Im going to drain fuel tomorrow, also going to check crank to see if its in phase(guy on PWCtoday brought that up and it makes sense). Im really gonna kick my self if i missed that when I took it apart. I was pretty set on the engine failing the leak test so badly that it had to be the cause of all issues. luckily I have another crank, but probably going to have to get a new gasket kit, at least for the base gasket. Thinking for checking crank phase I can mark the flywheel at front cyl TDC then rotate 180 degrees and see if the rear cylinder is on TDC. Any thoughts on that for accurate checking of crank phase?
 
I just replaced crank seals, this is me fireing up the engine after complete tear down and reseal of the engine. Checking timing and crank phase tomorrow when i get some time. Hopefully I can figure something out.
 
Messed with this thing all day. drained fuel, put fresh fuel in. Pulled tank did multiple flywheel changes and timing advance/retard. Everything I did off the stock position made it worse. Degreed(sort of just marked the flywheel in 4 places) the crank and it looks close enough to me. I got frustrated swapped ebox with a known good one. didnt work. I have ohmed out that stator a few times and it was with in spec. So out of frustration I just swapped it with a known good stator and also the flywheel that was running on that stator. Bam. Works now, revs so much easier, not popping. I got the thing torn to peices right now and have to put back together, but I believe and hope I found the last issue with this thing. This ski has been throughly molested today.
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