IH 460 running rough issues, any ideas?

Welcometo ATF!! Im somewhat confused, youre saying its only running on 2 cylinders?? Anytime you pull a wire off, it should skip. You do have the wires on in the right order?

Got spark on 1 2 3 4?

Any luck this this problem my 460 has the exact same problem. I think it is the intake manifold i took the manifold off and the front intake flange is not ligned up with the other flanges, it is set off the head by about 1/8, I was told there is a specific torke pattern does anyone know what it might be. Also the firing order is stamped on the block but which cylinder is number 1 the rad end or the driver end?
any help would be greatly appricated, This tractor ran smooth as silk before I took off the exaust manifold to weld a pipe on to support the muffler.

#1 is at the front / radiator end of the tractor.

I finally got some parts and replaced the exhaust / intake manifold gasket. chased all the threads and installed the manifold. The old girl started right up and ran smooth and quiet. Must have been a vacume leak. The plugs are wired with number 1 at the rear of the engine, I tried wiring it the opposite way with no good results. Anyway back up and running, next project replacing the wiring and installing a block heater or two gets pretty cold up here in Thunder Bay.

Mark Luke