99 Cobra Gear Swap?????

Most of the time a .03 shim on FRPP gears will get it close. I think it may be something else. You should have installed a new crush sleeve on your pinion gear. You have to crush it down by tightening the nut on the pinion gear. It takes close to 150-200 foot pounds. Once you get it close, you have to put an inch pound torque wrench on the pinion nut and check the free run torque. With new bearings it should be about 17-19 inch pounds and 13-17 with the old bearings. You have to be carefull and not go to far. Just take it slow and alternate between crushing the sleev and checking the free run torque. I think the pinion is not seated enough.

I think either the races aren't seated, the bearing isn't seated against the head, or you've tightened it too much. Usually, the torque of getting the preload correct is enough to pull the bearing all the way on and seat the pinion races completely - if you replaced them at all. If not, I'd look at the pinion bearing not being seated on the pinion head. By all means, you'll have to replace the crush sleeve and start over.

Did you use the stock carrier shims? You can't always get away with that. CLick on my site below under "IRS housing rebuild" for the proper procedure.