25" vs 30" shaft differences. conversion same as factory in every regard?

[chevy355mark]

I have been having a lot of trouble figuring why i have one outboard that's stronger then the other as some of you may have seen my other threads, sorry to keep dragging this out but I've got no solution and no testing left to do so let me just ask this one quick question.

is there any differences in a 30" vs a 25" with the 30" kit installed? will there be differences in the exhaust tuner in any way? would there be differences in the exhaust tuner between certain serial number break points?

one of my outboards is a xl and one an xxl. both 30 but one converted, likely from a set of triples that one was sold from. One outboard i could swear is noisier at idle. another odd thing i notice is that both power heads do not have the same hardware. One has all flanged cap screws and the other all standard cap screws with washers. I know how stupid that sounds but its clear they didn't come from the same production run, or maybe one just has a newer power head.

they are 1998 mercury 250efis. All the normal problems have been checked, cleaned, etc. Reeds, injectors, vsts, stators, cdms, computers, sensors, fuel pressure, timing, tps, bleed hoses, compression, it all checks out tip top. yes the props match, yes the lower units are of the same ratio(best i could tell anyway)