Well, don't feel alone, these stupid carbs are a royal pain in the neck, why the heck did they change from the almost bullet proof carbs with the metal bowls? Oh well, guess we all know the answer....
So the engine runs OK with an alternate carb, good info, and it has always run like this since you got it....That stupid primer has three positions, off, enrichment for warm up, and prime....I am assuming you are pulling the primer knob half way out to the enrichment position to keep the engine running.
The initial problems with these carbs was the funky rubber hose that connects the main jet plastic fuel pick up to the carb low speed tube. These hoses disintegrated, created an air leak causing the engine not to run on its low speed circuit. The hose debris also had a habit of plugging the idle pick up tube also, so the engine wouldn't idle even after hose replacement.
Does your engine still have the original plastic top set up:http://www.marineengine.com/parts/johns ... Carburetor
The ill designed low speed needle is hidden behind the air box, so the air box must be removed in order to make adjustments.
Replacement plastic tops have the side mounted low speed needle:http://www.marineengine.com/newparts/pa ... OMC0436342
So, if things are mismatched, there might be a problem...
Will the engine run on its own (no primer) at higher speeds? Keep in mind these engines won't run at high speeds without the air box/gasket installed, they will be lean which is normal.
Finally, and I guess I should have led off with this, synchronizing these crazy engines is another lesson in over engineering. Unlike just about every other OMC outboard, these carbs are designed to idle with the throttle valve "cracked open" just a bit, which is what that spring loaded screw is for on the throttle arm. There is a base timing setting as well, which requires checking TDC and a timing light. Do you have the synchronization instructions? Final adjustments are "ticklish" at best, because slight adjustments in the needle valve often require a tweak of the cracking screw as well.
You mentioned this engine runs/idles OK with a different carb. What style carb are you using as a substitute? Metal bowl carb from an older model, or similar style plastic top carb?
Sorry to post more questions than answers here, there are just many possibilities. Feel free to post pictures if that will help. D