Patrick Lawrence McCulloch

Trying to make this short but difficult. My son purchased a 2011 silverado 1500 4x4 (Texas Edition) 111000 odometer so far in six months we have had the transmission rebuilt replaced motor mounts and now after carring to get an alignment we were told needed upper control arms and ball joints inner and outer at a price Of $1600 I cried bs my son picked up parts for around $400 and we put them on not too bad carried back to dealer not gm and they said ball jounts wrong and could not allign front end seems like the bolt part of ball joint end went to far into spindle like the hole in spindle or nuckle or whatever is to big in diameter. Truck has around a 4-6 inch lift. The cassel nut tightened up so far carter pen hole below nut. My question is the lift kit or spindle aftermarket and maybe built different than stock and the bolt that attaches the ball joint end to the spindle needs to be larger diameter so called suspension expert a ford dealer stated he felt the spindle hole had wallered ( not a word) out making ball joint go to deeply into spindle. any help appreciated sorry for length of post