Did you have an .030 restrictor pill in the return line?
Regular BN carburetors work just fine if they're set up correctly. Most of what you hear and/or read on these forums and the net about them being "junk" is from lack of experience from the user. The regular BN carburetor was designed by Mikuni specifically to be used on the 550, with the mechanical rev limiter. If the rev limiter is bypassed or removed, an .030 sized restrictor "pill" has to be installed into the return line going to the tank, or the carb body will not hold fuel in ample volume long enough for it to reach the bomb sight of the carb. i/e, the fuel will run straight through the carb body and back in the tank.
Also, the initial settings for that carb are as follows:
High speed: 15/16ths of a turn out from closed.
Low speed: 1 and 1/8th out from closed.
Pilot: 1 and 5/16ths out from closed.
pop off should be around 17 psi with most a/m flame arrestors.
Stock flame arrestors are most generally restrictive to airflow, so they created super high manifold pressures, so the carbs are set up from the factory with a high pop off, usually around 24, and I've even seen them as high as 30 psi. If your intake filter setup isn't restrictive like a stock setup, and the pop off is set too high, this could also starve it of fuel.
That, coupled with the absence of the the rev limiter and no restrictor in the return line will definitely cause the problem you described, as either one alone would cause it to exhibit the same issue.
I've used regular BN carbs on 550's for 25+ years and have never had anywhere even close to the problems with them that I've read about on these forums.