If you have two tanks run two 5/32" fuel transfer (feed) lines form tank 1 to tank 2 . This makes it easier for the pressure to move fuel from one tank to the other . I have also wondered if using a larger dia. pressure fitting would help deliver a little more push to keep the fuel transferring easier . Andy , Dick ?
In our tank systems "Head pressure" has a real effect. The mixture WILL get leaner as the tank empties. No exceptions!
A full tank will exert more pressure at the needle than a 1/4 full tank, regardless of the location of the tank, HIGH , LOW, FORWARD, BACK. The changing head pressure, will ALWAYS change the flow.
A two tank system will go leaner as the first tank empties. Once the first tank empties the mixture will instantly go richer and then gradually go leaner again as the second tank empties. The size of the cross over lines will effect how much richer the engine will run once the first tank empties. The reason is because fuel is moving through the cross over lines when both tanks are full. Once one tank is empty, then only air is moving through the cross over line. And air moves much easier than fuel. The larger cross over line will reduce the amount of change once the the first tank empties.
This is very noticeable if two equal tanks are used and a good portion of the run is made on the second tank. The best situation is to have one Large tank that will not empty during the run and a small header/surge tank, then this instant richness will not happen until very late in the run. I mention this as a matter of record only.
I don't think it is part of Samuel's problem.
Samuel, I would say that your speed gain is caused by the engine/pipe temp increase and head pressure reduction during the course of the run. This happens in every boat. Some a lesser change, some more change. I suspect you are running one large tank and one small tank, correct?
Now that I explained the WHY, maybe someone can give ideas on how Samuel can improve the situation. This is obviously a Sport 45 hydro.