Welcome to DOOTalk. Great sled (I might be a little biased).
Sounds like you have done everything right, especially if you have spark. Even with a finnicky calibrated module mine would kick over and run (albeit not well). When trying to start the sled with fuel in the cylinders, were you cranking it over by hand or with the starter? My dad’s ‘96 Touring 440 used to act dead during the first start of the year when cranking with the starter, but would fire right up with a few pulls of the cord. It’s worth a try to pull it over by hand and see if that makes a difference. I have no idea why but it worked on that old 440 fanner.
Silly question but did you make sure the exhaust and intake were both clear of any debris, rags, etc.? I’m sure you did but it’s always good to double check.
What numbers are you seeing for compression? You noted one seemed a little low. Even with one lower in compression it should try to fire as long as it’s not way low like with a popped piston. You should be seeing 110-120 psi on both sides. A few psi difference from one side to the other is not unusual. 10+ psi difference would not be ideal though.
Also, when installing the new pistons did you make sure to gap the new rings to specs? They usually need to be filed down a bit. That shouldn’t affect initial kick over though. Just another thing to make sure was done.
You made sure the pick-ups were in the correct positions? The reason I ask is because if they were swapped inadvertently you could be getting spark but with the wrong timing.
Were the plugs wet when you tried to start it the first time (i.e. before you poured gas in the cylinders)? If you definitely have spark and the pick-ups are correct, then the only other place to look is fuel supply.
I’ll keep an eye on this thread. I’m also available to chat via PM if need be. We should be able to get this figured out for you. I rebuilt my 550 from the crank up the season before last. My mag side got ground up badly when a piston retainer circlip grenaded. I didn’t need a new crank but I had to replace the two outer PTO side bearings (the inner bearing had lost its seal and was washing away my Isoflex). I replaced a cylinder and head and put in two new pistons. It’s been running like a top the past 1-1/2 seasons since the rebuild.