front end problem

By looking back threw some pics i found a problem with the front end of my car, i had the upper a frames relocated, diff lenths, diff ball joint lenths, diff spindle heights and pin heights etc. The problem that i found was that the mounts that were used had 2 sets of holes, 1 inch apart up height wise. When we started the year off both aframes was bolted in the bottom set of holes, and about half way threw the year the front end was taken apart and put back together, the control arms was put in the upper set of holes taking alot of angle out of the uppers. It wasnt noticed because i am used to stock mounts with 1 set of holes, a big mess up on my end i know. With that being said im not up to date on all of the front end tech, could that have been a significant factor in handling issues that i encountered at the end of the year. The uppers went from being up hill to pretty much level