Thats a bummer abut the cutters being off. When I was doing my kitchen doors recently I brain farted and didn't allow for the tongue on the rails. It worked out where each set went down one size and I had to make new ones for the smallest sets of rails.
I number on the end grain then once I have the joint cut I start labeling the tenon and mortises. I have gotten pretty good at writing legibly inside a mortise. I use a number and letter on everything, i.e. 1a, 1b, 2a, 2b, so matting mortise and tenons will both say 1a.
And like you said it is a matter of coming up with your system.