Yep - there is a notch for the clip so they are in a fixed position. You'll have to drill. Pretty annoying as you say - these are way off. Alternatively you'd have to add a notch to the guide to align Mirco's hole which seems much less desirable.

Locate the guide as best you can, drill to just start the hole and then move the guide to finish the hole so the guide is out of the way. Many of the guides on Spirit only convey the ball to the rest of the playfield so position isn't critical as long as the ball goes through. If you need pictures, let me know.

I own two Spirits and I just noticed that at one metal guide I checked, the playfield attachment location and corresponding groove for the clip in the guide are in different places between the two games! The guides are actually different! Apparently some changes mid-production from Gottlieb on Spirit.