Adding windage tray to assembled short block

No. Not if you are replacing the bolts with studs. The mains normally require honing when that's done.
I have done it countelss times using the MP package and bolts including the 360 in my truck while it was still in the truck. But studs load the caps differently and at minimum I'd want to carefully measure the main bearing bores after you torque the caps on those two spots. Plastigage may not not show the distortion so I'd say you're safer to run without it if you're not going to do it right.
Or get the MP pacakge and use that one.