90HP Yamaha with two dead cylinders

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?

Did you clean the dirt out of the inlet on the carb that is blocking the float needle and seat?

Nothing is blocking fuel flow. All fuel lines from tank to engine were replaced. Fuel lines inside cowling were flushed when fuel pump and filter were cleaned. Bottom carb was cleaned but engine still run on only one cylinder.

Docksidemarineservices said:

Did you clean the dirt out of the inlet on the carb that is blocking the float needle and seat?

Click to expand...

This is inside the carb where the fuel line connects.