90 HP Yamaha running on one cylinder

[Broadhead]

1999 90HP Yamaha Jet Drive (90TJRY) low hours, started running rough at low RPM. Found that the oil pump end of the control rod (plastic) from the bottom carb had broken and allowed the oil injection to go to max. Replaced linkage part and cleaned plugs. Still rough.
Found some debris in fuel tank. Replaced tank, lines, bulb, cleaned filter and fuel pump. Still rough.
Replaced plugs and tested spark with in-line tester. Spark strong to all cylinders. Found only top cylinder was firing.
Ran compression check (116, 118, 117), not bad.
Because bottom two cylinders were not producing power, pulled bottom carb, inspected, cleaned, and reassembled. Carb was very clean with no evidence of blocked jets/passageways. Still rough.
Any ideas?

[jb123]

Spark strong to all cylinders. Found only top cylinder was firing

what does this mean ?

[Broadhead]

That means that all three cylinders have strong spark but only the top one is producing power. The bottom two are dead.

[99yam40]

If compression and spark are good then you need to be looking at the timing and the fuel/air mix