If they won't go all the way on is it because the inside of the cap is hitting the end of the spindle or is it because the stem of the cap (the part that presses into the bore) is longer than the original?

I've had aftermarket caps that won't go all the way in up to the flange on the cap but it was because the bore in the rotor wasn't as deep as the stem of the cap (behind the flange). Once I ground off about 1/16" - 1/8" from the "bottom" of the cap it pressed all the way on nicely.

I ended up using shallow caps.

They still took a lot of work.

I will take them off and use a toothpick to measure the depth. one cap went on further then the other so something is not right. ran out of propane so tomorrow after work i will revisit the problem

i do recall from the past, that some replacement rotors didn't have the same machined depth for the dust cap;
Personally, I liked it when there was a small gap between the lip on the cap and snout on the rotor - because this made it easier to R&R the cap at a later date.