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1989 Indy 500 idling one 1 cylinder

Rebuilding last machine (1989 Indy 500) for the grandkids. I have stripped everything down and gone through everything. Tore carbs down and cleaned all passages, jets, needles. Dropped engine in this past weekend and fired it up. Starts and runs only on one cylinder (mag side). I have good spark, good compression and fuel to both cylinders. When I pull on the choke cable going to the cylinder that's not firing it then fires up and runs as long as I'm keeping rpms up. I sprayed WD40 around pto seal but that didn't affect anything. I then swapped carbs, leaving fuel and choke lines and cables attached and the problem does not follow the carb. Any suggestions would be appreciated.
 
So it runs when you provide more fuel which kind of points to an air leak. Can you spray WD40 around the carb boot on the PTO carb to see if that changes things? How about the reed valves or does it have them? Swap the plug wires just for kicks to see if that changes anything. Both plugs fire at the same time anyway.
 
this is the old Fuji piston port engine. I haven't swapped plug wires (will do that) and I sprayed WD40 on pto end crank seal. Didn't find any carb boot cracks but will check more thoroughly this afternoon. Thanks for the suggestions.
 
When you say you stripped down and went through everything do you mean the engine too? The reason I am asking is because a broken piston skirt will cause a similar problem. It wouldn't show up on a compression test.
 
Try swapping sparkplug leads like bushwacker suggested, Maybe change out the caps.
 
Got to checking further and found that crank seal was bad. When I split the case to replace them, I found that the PTO bearings had given up the ghost and will be replacing them in near future
 
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