951 swap and now issues

I swapped an engine from a 99 XP Limited to my 98 XP Limited. Replaced all seals and rebuilt carbs when I did it.
The issue is: When I go to start it, it cranks for a few seconds then stops and then restarts all while holding the button down. I put some fuel in the cylinders to get it to fire and it fired but the crank is weird. It is not a constant crank and I am not sure why it would do it. I am using the MPEM from the 98 with the 99 engine. I haven’t read anywhere that said I needed to change it.
Any ideas are appreciated.

Also, what is the trick to priming these carbs so I don’t crank until the battery dies.
 
98 and 99 used two different ignition systems. 98 is a single coil 99 is a dual coil. They use different mag cups.
 
98 and 99 used two different ignition systems. 98 is a single coil 99 is a dual coil. They use different mag cups.
Learning new things daily. I have the control box where the starter and plug wires come from. I assume I need to swap that too then. Anything else need swapped?
 
98 MPEM with 99 engine… You need to use the 98 mag cup. Mag cup bolts to the fly wheel and has magnets that trigger spark. the shop manual will show you the correct orientation.
 
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