If you tightened the bolts before it was back on the ground then yeah, it could be riding crappy because of that. It may have preloaded the bushings so they are biased towards downtravel and they are really resisting further up travel.
Loosen up the three nuts on each leaf spring/shackle so they are loose but won't come off, drive it around the block slowly so things settle back to neutral, then retorque to 40-50 lbs + use locktite like others have suggested.
Also make sure the shocks are oriented the right way. That will give a rough ride too if they are upside down.
'94 YJ - SBC/AX15/231, SOA, 8.8, 34" swampers
'06 LJ Rubicon - 31" ATs, OME 2.5", belly-up skid, other junk
'75 CJ5 - 232/T14/D20, 'glass tub w/ 2" BL, otherwise stock