Sam,
Stick with 25 yards until you are consistent, point of aim, point of impact (POA-POI).
1. stance: are you resting the barrel on the bin, or just your wrists?
2. bullets: the Rainier bullets are made for a max velocity in the range up to 1200-1400 fps. If you exceed that, the bullets may be fragmenting. This does not mean that they will shoot low, just randomly. I use them in my 50AEs but keep the vels. to 1400 fps or less, with great results. I've used the HPs hunting whitetails with good results.
3.scope: most boresighters, not necessarily the lasers, are not made for short guns (handguns). They're OK for windage adjustments but not for elevation. Also, if the scope is mounted properly, and rings are secured to the scope and the gun (no movement), you should not have to travel the extremes of your scope turret settings (windage or elevation). I assume that your 50AE has the Picatinny / Weaver rail integral with the barrel. It is possible that your scope is defective, not allowing adjustment and repeatability. You may need to try a different scope, after inspection of the rings.
Your rounds should'nt drop that much from 25 to 50 yards at 1350 fps. Are you using magnum pistol primers? What powder and how much? I use H110 (WW296), 30.2 grains, Win large pistol mag primer, Speer brass, Rainier 335 gr TMJTC/HP bullet. In my FA 71/2" revolver I'm getting 1400 fps., 1 -1 1/2" at 50 yards, with an IOR Micro Red Dot optic. This load is slightly compressed, making the powder a little more difficult to ignite. If you get inadequate ignition / incomplete or inconsistent burn of your powder, you will be tossing whiffle balls. However, you would be able to tell that from the report (recoil, etc.)of the round.
Hope that helps!
Doc