<<I don't think an alignment machine will pick up an offset wheel difference?>>
If not then you are going to have issues. The string setup does require all wheel tire combinations to be the same if you want accuracy. You also need to take track difference into account which might mean installing 5 mm spacers up front while you do the setup. If the tracks do not match the tow numbers will be off.
Frankly, I think Bruce hit the nail on the head. CASTER MISMATCH.
<<I also discovered that one of my wheels is a different offset. Yep, you read that correctly. I spent a good long time going over all the suspension components and subframe trying to figure out why that corner was 5mm "shorter" than the other.>>
Alberto, if I am reading you correctly, I think you misunderstand something here. 5mm of offset difference on one side of the car (driver's side in your case IF I am putting it all together right) will not give you 5 mm of toe difference. PM me your phone number and I'll give you a call. Too much for a post.
FYI, you can check caster with the strings. You will need turn plates or two floor tire/grease sandwiches for this. Set the handbrake if you have one or block the rear wheels if you opt for the grease sandwiches.
1- Get both front tires pointing equally forward (i.e. match toe side to side)
2-Measure camber of both front and note
3-Turn steering wheel EXACTLY half or 3/4 of a turn to the left and lock in place (tie down works well)
4-Measure camber of both fronts again and note
5-Repeat 3 and 4 with wheel turned to right by same amount as in 3 above.
What did you measure side to side?
The side on the inside, or unloaded side of the car in a corner, should not have changed camber much if at all compared to pointing straight forward.
The side on the outside, or loaded side of the car in a corner, will show a camber increase. Both sides should show the same increase unless you want to get into some more advanced setup techniques.