OK, if you haven’t already started the big print…
If you print the tool mounts with the router diameter about three mm oversized, you could then print two concentric inserts with an offset centre the correct size - to give roughly 1.6mm of offset on one side compared to the other.
Insert one in the top mount and one in the bottom mount and simply rotate them until the router is perfectly trammed.
Should I patent this idea, or just let you see if it works before I get too excited? 
If it works I’d put a little 45 degree flange on the “inside” edge and a matching one on the tool mount to make it captive.