I've had no time to deal with this until yesterday. I pulled the headset apart, compared it to the old headset once again just to verify it really did match up with the specifications. The seat cap from the bottom bearing matches and could be swapped between old and new bearings. The old seat cap for the upper bearing is slightly different in design to wrap around the bearing more, but still matches dimensions. I replaced the new bearings and seat caps, added a spacer under the stem, and swapped out the compression plug for one I felt would protect better and have a more typical top cap (cap+bolt rather than cap being tightened to the compression plug). Once everything was back together, the gaps remained, but everything was tight once again. I left it alone as the bike was going back on the trainer anyway. I've got enough maintenance to keep up with on the bikes I actually ride outdoors without adding another into the mix anyway.

Appreciate all of your help and advice on the subject.