No, it's not leadscrew specific. You want to check this without the carriage engaged, feed or half nuts.
As for class 3 bearings, I've never had to replace any spindle bearings in the lathes I've had over the years. My dad replaced a double row tapered roller bearing on the head stock of his Axelson lathe that was a class 3 bearing. The original bearing had water damaged from when the lathe was on a navy ship that was sunken in WWII and salvaged years later. You will never notice the difference between a class 3 or 0, 00 Timken bearing on a lathe. And we used to do some tool post grinding on that lathe that left very nice finishes, too!
One other thing you can try related to the lead screw. Remove the leadscrew support on the tail end of the leadscrew. Engage the half nuts on the lead screw. Do this out on the tail end of the leadscrew. Slip the bracket back on the shaft and see how close the bolt holes line up. Should be pretty close if not right on. Also attempt this at the QCGB end of the leadscrew too. Since the lead screw will be hanging and flexing, this may be a little harder to detect alignment. If it's out any at all, it should magnify as a bunch of movement in the leadscrew when the half nut are engaged. Also, the leadscrew bracket may or may not line up very good, maybe even to the extent, that you can't get the bolts back into the holes.
Is this the Quick Change gear box you replaced the gear in? If so, this could be your culprit.