I used the factory guide holes when I put the subframe back on but later decided to use the factory alignment measurements in the Service Manual. Glad I did - using the guide holes is a rough approximation in my opinion. The most important measurement is the cross one from the rear corner of the subframe to the opposite rear frame rail.
When I did it the 2nd time, I had did not have any of the front clip on and would think you could be shifting enough to cause front clip sheetmetal to kiss the doors or something else.
2012 Mustang Boss 302 #1918, Competition Orange. FGF replacement 2006 Mustang V6 Pony, Vista Blue. Factory ordered. 2019 BMW X3 (Titled to the wife, but I'm always driving it for her. So I'm claiming it) Old projects, gone but not forgotten: 1967 FB 400, original CA car. After 22 years of work, trashed by the guy who was supposed to paint it. I had to sell it. 1980 Turbo Trans Am 1970 Mustang fastback, 351C 4Bbl, auto 1988 Mustang GT, 5 speed 1983 F-150 4x4, built 302 1994 Chevy K2500 HD 4x4, 454 TBI