1980 XS400G Won't Start - Uneven Manual Crankshaft Rotation

[CrashGard]

Hello All, long time reader, first time poster. I have really appreciated the information on this site but now i am stuck so need some directed help. Background: I bought a non-working 1980 XS400G Special II. The starter motor drives the engine but it just won't catch. I have cleaned the carbs, bought a new battery, checked the spark, cleaned filters, etc and it still won't catch. I took the heads and cylinders off, cleaned everything, honed cylinders, lapped valves and put it back together...no change. So here are my questions (for those who wouldn't mind helping out a lost soul):
1) When manually rotating the crankshaft when the cylinders are off, it was very smooth and even. By the time I installed cylinders, heads and the camshaft cover, the manual movement of the crankshaft is rather uneven. Is this possibly due to the valve springs? Should it be even and smooth?
2) I didn't connect the exhaust...that wouldn't stop it from starting...would it?
3) If there was a ground issue, there wouldn't be a spark...right?

 

[CrashGard]

4) As an additional question to help narrow root cause, with the exhaust system removed and the fuel mixture correct, if there is no combustion in the engine, shouldn't the exhaust be flammable? I thought to put a flame on the exhaust port but it does not flame up when the exhaust passes through the flame. Does this point to an incorrect fuel mixture?

 

[CrashGard]

More background:
1980 XS400G Special II (3F9)
Purchased non-working - Electric starter turns engine but won't "catch"
Cleaned Carbs - New Battery - Checked Valve Clearance - Honed Cylinders - Lapped Valve Seats
Checked for Spark (unseated plug and rested against engine during start to see spark)
Good Compression - Timing (ATU - cannot check until running but visually checked)