I just finished installing a 3" spacer lift on my TJ ('01) and I can't get the rear trac arm to line up with the bolt hole.  Any ideas???  

I'm guessing since it's a 3" spacer lift, that it is an incomplete lift. That amount of lift requires more components than just spacers. It is not cheap to lift a TJ 3" and have it still drive correctly. For 3" you will need to at least address the track bars front and rear, driveline angle, sway bar links and shocks. The rear track bar won't line up because it's working length is too short. An adjustable track bar or extension bracket should be used. JKS, amoung others, makes a bracket and it is less than $50. The problem with extension barackets is they increase the leverage on the original bracket and break them off the axle. Inherent in the TJ rear suspension design, the upper control arms and the track bar bind when the suspension droops.

So, you can loosen the UCAs, put the jeep on the ground and use a ratchet strap to further compess the rear suspension and the track will come into line.  

yeah...with the 3" I wouldn't even attempt to get the track bar hooked back up without an extension..
without the extension the axles will be off tracking.

here is what hapened to mine from an extension..bear in mind it was not from "normal usage".
the track bar extensions are safe to use..


 

Isn't this image is of an upper control arm extension?



Look for a hefty track bar extension and consider gusseting the stock mount.  

its the rear trackbar mount, the left side upper control arm also bolts to the same location.  

Thanks for the help.  I decided to try out the brackets for now $$$ stopped me from going and getting the adjustable track arms.  I just won't do anything crazy till then...