Ed
We have H54 - #22. We repowered in 2016 with the Yanmar 110hp common rail. Did not have the problems you are experiencing, but with the larger engine, you have significantly more fuel flow then the original engine. Makes some sense you are getting larger drops.
On our engine, the lower levels on the fuel tanks were below the recommended lift on the new engine. I think it specified no more then 2 feet and we had closer to 3 feet. In discussion with Yanmar, we installed a small, low pressure booster pump on the fuel line between the fuel manifold and the engine intake. Did a bunch of testing for yanmar and we were all happy with the results. This may help your engine by keeping better pressure at the intake, but will probably not solve the fact you have more than expected drop across the filters and manifold or air in the lines. The larger manifold valves may be an easier solution to reduce pressure drop. Our experience with air is that it has to be getting in someplace, via loose connection, gasket, etc. The higher vacuum will cause more air in the line but the root cause must be something allowing air in somewhere in the system.
Let me know if you are interested in any additional details on our booster pump.
Scott Johnson
SV Bacchus
H54 - 22