seahorse

just for the sake of discussion, have you looked at other brands of outboards for your boat? Here is a link to a recent video of an accurate comparison between the brand new Merc 150 and the established Evinrude E-TEC 150

A 1990 powerhead is a different block design than your original '98 powerhead. OMC redesigned the big block 3.0L engines in 1993 and improved other items and introduced them as the Ocean Pro and Ocean Runner models. Have an experienced tech check over your powerhead to see if it was a jury-rigged replacement or if it is not what was represented to you.

Was a new oil pump installed with the crankshaft sleeve installation or at least were the pump's oil seals and o-rings replaced at the same time? If not, then the corrosion on the crankshaft which caused the leak in the first place, probably damaged the oil pump seals and that may be why the engine is still leaking oil.

Many of them have an L stamped on the end of the propshaft

When you add an additional gauge to the fuel sender wiring, you are changing the "load" and resistance on the circuit so the gauges will either not be accurate or not be operational.

possible air leak in the intake hose connection?

There is an air motor diaphragm and a fuel pump diaphragm, various flapper and check valves plus an oil piston pump and the alarm electronics. There are pressure tests that can be done plus flow tests, alarm tests, and priming tests, all in the service manual. This may help and it has a great picture of the insides of the pump: http://continuouswave.com/whaler/reference/VRO.html

How did the other diaphragm look?

On how many websites have you posted the same question and images? There is an oring under the cover of that plus a needle valve and float. Use the service manual procedure for setting the float level after replacing the valve and cleaning out the fuel cavity.

A sharp trained tech can fix you up using your original harness and just adding the engine drop cable, boat network, and digital gauge(s)

Talk to some authorized dealers. They can check the factory parts database to see if other dealers have them in stock, plus there was a bulletin about replacing ones that fogged over from some years ago. I believe, but not sure, that they were made by Faria Gauges and you might contact them.

If you were using the round ear muffs, that may have been your problem. The rectangular ear muffs have a better fit over the Yamaha inlet screens. You should also use a dual feed flusher for best results. The hose on the motor with the garden hose fitting is NOT for running the motor. It is only to have water fill the block and wash it out. Read the owers manual - do not use that hose and run the motor.

Besides all new cables, controls, gauges, and wiring, you may have to fill the transom mounting holes and redrill them farther apart to fit the Yamaha motors. Likely your engines are at 26" centers and Yamaha V6's need about 27 1/2" centers to clear each other. That may also put a bind on the rigging cable on the stb. engine if it hits the edge of the end of the transom. Measure carefully before committing to the motors.

That article is exactly why the outboard and oil companies got together and "designed" the NMMA FC-W oil certification protocol for 4-stroke outboards. Modern car oils have lower anti-wear additive protection due to the EPA's concern about wanting catalytic converter effective life to be longer.

The first thing to do is get rid of the battery wing nuts and use stainless steel nuts and lockwashers tightened with a wrench. Then check the battery cable fastening at the motor. Your motor stumbling when trimming is due to lack of voltage to the ignition and electric fuel pump and injectors. Somewhere in the electrical system is a "restriction" or your batteries are weak. Yamaha does not recommend the use of maintenance free or sealed batteries. In very rare instances, the stator could be weak or the regulator acting up.