I have a pulse xt 40 pnp modle with a evolution .46, the manual says to use a 11/6 prop. Can I put a 12.25/3.75 prop on it to make it come in for landings a little slower? I know I'll loose some top speed, but I would rather fly slow.

Yeah that will be fine.

The plane has a fairly low stall speed anyway, so the slower prop is not going to be an issue.

I have a pulse XT 40 with a OS 55AX and I fly it with a 12*6 APC prop. I find it a good combination. Landings are fine.