You can't do that, unless you have 0.0 angle at both ends, only race cars can you check for run out.
This may not come across as why but i'll try and explain it. Angles on street cars are there to circulate needles and that circulates grease and expels the old and brings in the grease kinda stored in the joints cavity.
When the shaft turns the joint oscillates, as it oscillates it is pushing the shaft forward and back, and as it does that the shaft will lets say wobble.
This is something i have gone thru and do go thru still with many shops today, i tell them all the same thing, if you check shafts like that and i don't double check you, you will be putting a new shaft in every customers car you do that with.
If you had removed the angles like a race car you could check that, otherwise it's going to show something that isn't right, i had a shop call me and tell me a shaft i just did had .012 run out like the old one, and i told them that particular shaft has .002, i said if you bring it down because i know what i did and that im not sending my truck to pick it up and for a $50 bet i'll put that shaft in the machine and check it in front of you, if it's more than .002 the shaft is free.. I made $50 and had to show them what happens in a car.
There will always be some movement at the bushing also.
Stick it in and lets see what happened with the new bushing, balance and setting the pin to be at 0 with the shaft under load