Engines have a Recommended WOT RPM range. examples; 4500 - 5500, 4800 - 5300, 5000 - 6000. At 6100 you are probably over revving, but by how much? You haven't provided the WOT range speced by Yamaha. You also haven't provided any info as to what prop you are currently using. The info is on the prop, you just haven't located it.
"boat originally came new with a 200hp.when I got it, it has a 250hp.thought maybe the 200hp prop might have got used"
The two engines probably utilize the same prop(s). Depending what the gear ratios are on engines, they may or may not use the same pitch on a given hull load, or they may require different pitches.
"hole shot is good and up on plane is quick but if I pull back to bring the motor down a little it falls right off plane."
You are falling off plane with the engine at 5500 rpm? Something here is not adding up.