I picked up a two piece hard top for my 95 Tracker but the rear glass was broken out hence the excellent price of $95. Where would you suggest I start looking for a replacement glass (dealer or aftermarket) other than Lexan. My local glass shop said they only have a number for a glue in rear window. Any help greatly appreciated.

depending on the top i have a back window that mounts to the tailgate

If it looks like this, with or without roof rack, and has 4 screws holding the side glass in , then it's a Bestop and they no longer carry parts.  You'll probably have to improvise.  Good luck and please post your fix.

You could have a piece made and tempered or go with a polycarbonate
replacement, that's what aircraft windshields are made of

Wild

I would make a cardboard template and cut new replacement windows out of lexan and use 3M Windoweld to glue it in.

Starting on my fix before the snow flies.  I was lucky, already had the window weld (was going to glue the hood cowl trim on my sister's '99 Concorde).  This is my other Bestop hardtop (sans roof rack).  I tried the factory application by drilling holes at the mounting locations, but after 1 winter, the expansion/contraction stress cracked at the holes.  For sealing, I had used RV weather stripping.  That didn't seal very well due to the flexible nature of plastic (factory side glass is rigid).  I'm just mocking up for now.  I'll probably use double faced tape to apply horizontal 1/4" luan plywood rips across the clamp locations so to protect the plastic, distribute the force, and add shims, behind it, to apply force in the middle of the longer sections.  I gladly accept suggestions.  Thanks

1/4" plexiglass material would be less prone to flex and seal better

Thanks for the suggestion wildgoody.  I tested 1/4" plexiglass but it is thicker than the recess in some spots and sticks out beyond the hardtop opening, hence, no longer flush with the hardtop surface.  I'm committed to the 1/8" as the windows are already cut and rough fitted.  If this doesn't work I might try 1/4".  It won't be my 1st failure. 

The 1/4" plexi is stronger, and flex's less, but that will make install and retension an issue. Alot more clamping pressure will be required to get the plexi to make a uniform seal and it will more than likely distort the fiberglas top. I would clamp it into position and then use a heat source to heat the plexi and take the tension of being curved out of it. This will also make it less prone to shattering/cracking/leaking after the WindoWeld cures.

That's a good point, I had assumed that the original glass was a flat piece,
but if there is a curve in it, the thicker plexiglass might not seal properly 

Yes, the Bestop side glass is convex.

Finished product.

WindowWeld & clamped.  This should have preceded the finished product post.

Turned out nice, good job!

Thank you talonxracer.  HydroMachinist, I have 1 original side glass that I'm going to save, if you have a Bestop hardtop, I could make you a template and mail it to you.