I actually had a pretty big crack that shattered my window on the back passanger side of my hard top (damn tree....). I did pretty much what you said, I put on some epoxy (inside and outside) and then a nice black waterproof coating on the outside (can't remember what it was called...).
It looks pretty good, the only problem is the epoxy does stick out and it is pretty clear that it was repaired (adds character if you ask me). I may sand it down a little bit eventually, so have it blend in a little better, but at the same time I do like the rugged look.
I just noticed the crack myself. Plastic is hard to repair permanently. I'm thinking, Clean the crack area real good. Find some thin 1/8" Plexiglass, and make plexiglass patch. Probably 1" to 1-1/2". Question is what to use to glue it. Either Epoxy or an adhesive they make for plastic.
I did some plastic molding repair for Large Truck interior molding, using plexiglass and epoxy, and was surprised it worked.
I'm gonna remove the two tops and determine how many screw turns it takes before the screw hits the plastic from the inside. This will determine how many turns you can go when you put the tops back on your jeep. I'm pretty sure this is what is happening. I will most likely be making some thick washers so this does not happen anymore.
I took my 2 tops off to determine the max rotations it was and both were approx. 18 turns. And made a note of it with a Sharpee Pen on the covers. I got some Tool Box Shadow Foam and made washers. Now the turns are approx. 10 rotations when tight. Eventually the foam will get compact. But at least I know I have the problem and how to fix it. Also I cleaned the area on top where the small cracks are and applied some Black Adhesive Sealant.I hope thats the end of it.
Permatex Black Silicone Adhesive Sealant. I've also made the decision as to the tightness. Right now I go only Finger tight and I carefully watch as the covers start to press against the Jeep Seals when tightening the screws. I've also been making washers from Plastic containers and Plastic container Lids such as Folgers Coffee. And put alittle grease on everything. Keep us updated on this issue. This really makes me wonder, everyone has got to have this problem. I would not want to see what the price is for those 2 covers. I would imagine at least $300. You never did say how bad yours was cracked.