Those clips on the ball guide can slide along the edge to match the drill holes.

This is typical. There was a hole missing on my mirco whirlwind and 90% of my backside dimples were off by 3-4mm and I had to countersink a ton of holes that were missed.

But in his case the clips are adjustable so no new drilling is required.

Aren't the clips set into a cutout in the guide? I run into this kind of thing with ramps pretty often. Adding screw holes in a new ramp ahead of time is a bit of a crap shoot, because some of the attachment points into wood are located wherever Jimmy at the factory decided to run the screw in that day.

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.