Sounds to me like the shop owes you some time figuring out what they did.
No idea what your stick is like, but as part of a custom conversion I did, we just heated up the stick with a welding torch and angled it into the position I wanted. We made sure all gears were in a good place with no obstructions (dash, my knee, the Tuffy box I have in, etc.).
Of course this was a very different engine tranny conversion, you shouldn't have to do that putting on a simple 4" kit, but its an idea.
[SIZE="4"][COLOR="DarkGreen"][B]KNIGHT6 - '78 CJ5. [/B] [/COLOR] [/SIZE]
Ford 9" x2, Tru-Hi-9 High pinion, 5.14s, 2 detroits,
SOA, D44 'flat-knuckles' High Steer over springs,
Chevy 5.7L Vortec, Ford T-18 with granny-low 1st
37x14.00 Iroks, Warn 9K lb winch,
Metal Fusion tube fenders,full cage frame tie-in, +++