I've never pulled a transmission with the engine on one of these cars.
But wrx & 04 sti have dowel pins you need to punch out. idk if thats exactly the issue at hand.
As far as lining up the splines I use a lift with a transmission jack that has a chain to hold the trans to it, and two tilt adjustments. Works awesome. I'll also use a exhaust jack stand to tilt the motor back for extra angle.
I also herd you can just pull the motor forward to do a clutch need to remove the radiator of course. Idk what else never tried