So my bravo one has Xr upper gears, a custom tower,and billet top cap. I just bought the boat, and noticed it shifts into gear very stiff. Shifter is hard to push forward and reverse. Any thoughts as to what would cause this?

are you shifting it with out the engine running?? if so dont do that unless you have to..always try to shift running.

No this is with the boat running.

Check both shift cables, what is the idle rpm of the engine. Higher rpm makes it harder to shift.

a lot of possibilities,gears are not timed correctly in upper gearcase,control cables dragging,lower shift cables dragging,shift link cavity has water in it causing rust where the detent ball rides on shift link,what year is set up?

Boat is a 99. But drive was rebuilt/ upgraded in the last 2 years.

The shift linkage and detent assembly behind the back cover is probably worn.