First, never (!) turn the flywheel on a TJ. Its surface has a special slight dome shape that would be removed by turning/resurfacing it. The factory service manual warns against having the flywheel surfaced or turned. If the flywheel is damaged, it has to be replaced... but never turned or resurfaced.
The squeal is likely caused by the throwout bearing which is what the clutch disk spins on when you are holding the clutch pedal down. The throwout bearing is sealed and non-serviceable so it is replaced when it starts getting noisy.
Since you have to pull the tranny to get to it, might as well replace the clutch, pressure plate, pilot bearing, and throwout bearing all at the same time. Get the Luk OE replacement clutch kit (not the Luk ProGold) for around $130 or so from Dial-A-Clutch - Your LuK Clutch Kit Specialist
(which is where I got mine) which has everything you need.