Motorcycle Repair: 1997 Kawasaki Concours, high octane gas, ape cam chain tensioner

Question
Hi. Have been working on the 97 Kawi Concours for the past two weekends. Initial work was to check the cam chain and tensioner, check valve clearances, change oil, change plugs. Everything checked out ok. When we reassembled everything the bike was only firing on two cylinders (1 and 2). 3 and 4 were not firing. The strange part is that 3 and 4 are on separate ignition coils. Here is the troubleshooting we have completed:
emptied gas tank and refilled with high octane gas (from gas station).
flush gas through all 4 carbs by opening float bowls.
Lightly blew compressed air through the fuel input and ensured aid got through to each petcock when we opened them. Small debris came out, but nothing that indicates something is wrong with the carbs.
checked for spark and assumed the spark we saw was good.
tested the resitance on the primary and secondary winding of the ignition coil. They checked out fine. Changed the spark plug boots as some of them were oil soaked. Replaced the cam chain and installed an APE cam chain tensioner. We thought the wires coming out of the igition coils might be mixed up so we tried all combinations with no success, still not firing on 3 and 4. Tested for heat on the pipes to make sure we weren't crazy with multimeter thermometer - 1 and 2 were at 400 degrees farenheit and 3 and 4 were at 150 degrees.

We also installed a new Progressive shock only mention this because we did it. But the firing problem was discovered prior to the shock change.

Any ideas on the cylinders? We are stumped.

Answer
You didn't say why the bike was torn down in the first place, was it a runner before tear-down ?
You didn't say whether you checked for spark in those cylinders, but I would say that you have tight valves in those two cylinders and no, or very low, compression causing them to be devoid of combustion.... Kill two birds with one stone-pull those two plugs, You should pull all 4 plugs to do this right, put them in the plug caps, ground them, hit the elect starter.... is there spark ? When doing this be extra careful to not ignite the gas that might be forced out of the plug holes !!!!
#2 check the compression in these 2 cylinders... it might be very low or zero...you could have degreed the cam in wrong and your cam timing is off also, if it is way off this could have bent some valves but I bet this is not the case.
Lemme know...
Thanks !