I'd say one additional problem that you may have "developed" here is your shop mechanic's "belief" system. He "believed" that your lower carb was the culprit but reality proved him wrong. Now, he "believes" the top carb is the culprit....ok...let's HOPE he's right! Or, let's HOPE you're right with not taking a chance and doing the other carb. Which, brings me to my point.
You are the amateur here and HE is SUPPOSED to be the PROFESSIONAL. There is SUPPOSED to be a different set of rules that apply to the veracity and accuracy of and for each of your individual diagnosis. You took the job to him with that expectation I would think. YOU are allowed and, in some cases, including this one, EXPECTED to be WRONG. Logic and luck ALLOWS you to be correct OCCASIONALLY but being WRONG is what led you to this guys door. Ok, that's fine. That's how it works. That's how its supposed to work.
HE, on the other hand, is EXPECTED to be CORRECT and, of course, because any of us in any profession do make mistakes, is ALLOWED to be WRONG. BUT, and this is a big BUT, when he is WRONG, it is not your responsibility to PAY HIM FOR BEING WRONG! You went there to give him MONEY for being RIGHT. That is ALSO how it works.
He plainly and clearly DID NOT diagnose your problem correctly, that much should be TOTALLY clear to all involved or reading this. Therefore, in the name of all that is sacred between a shop and a customer, he should be making ALLOWANCES on YOUR BILL for HIS MISTAKE.
I'm not saying that he should work for free or that he should have his head held under water for not getting it right the first time. But, he needs to adjust for the fact that, when all is said and done, he didn't get 'er DONE. Your labor charge for the tear down and assembly that is coming should BE NOWHERE NEAR the one you have just finished paying him for. Yes, he can charge you additional labor for going back in and dealing with the added components but YOU ALREADY PAID for the privilege. And, it brings up another point.
Whatchu gonna do if he's wrong again? There are METHODS for determining what is happening with an engine when it isn't running perfectly. IN THIS CASE, it is a really very simple METHOD as well. It is called ARTIFICIAL ENRICHMENT. If he is going to hang out a sign and say "GIVE ME MONEY FOR FIXING YOUR OUTBOARD" then it is INCUMBENT upon him to be PREPARED and EQUIPPED to perform this simple test of adding fuel to EACH AND EVERY ONE of your carburetors when he BELIEVES there to be a fuel delivery problem. THIS IS MECHANICS 101! There is no need to BELIEVE, because we can TEST.
I say all of this because I AM a PROFESSIONAL MECHANIC and I would CERTAINLY NOT CHARGE you FULL FREIGHT for ANOTHER tear down. As a matter of fact, I WOULD BE EMBARRASSED if I had called this job this way.
What I'm saying to you is that I don't trust this guy already. I don't want to make you nervous but that's just the way I see it from here. And "here" is a long way off, I realize. I realize also, that you have to use your own best judgement to deal with this problem and this might be the only shop within miles. But, go back in this thing with OPEN EYES, watching like a hawk! Question his METHODS. ASK him if he's comfortable with charging you twice for an unfinished job. OR, print this out and let him read it. I'll defend my words if he disagrees. If he's honest and fair minded he won't.
Nuff said,
Good luck.