When I was at the sign shop, they had special glue for lexan. I don't remember what it was called, but I know it was strong stuff. It essentially melted the material some, and then fused it togther. If you didn't do that properly (as well) you'd get a weak joint/seal and have problems with it later. Caulk will only go so far too, before it can't handle what is trying to come out. Have you thought about [maybe] reversing the way the 3.5" bay res. goes into the case? Have the fill towards the inside, and run the lines so that they can come out the front (formally the back) and still work? You could, even, use some metal brackets to kick the res into the case more if you need to for the tubes to run without kinks (or get the kink-less stuff). OR, get elbow bend fittings for the res so that the tubes come out towards the sides anyway. You could even make them go down to the bay below and then to the pump/radiator... Depending on your case (as well) you could mount the res on the bottom of it (if there's room) so that all you'll need is a funnel, or funnel and length of tubing, to fill it/top it off.
You might need to get a bit creative to have the system fit as you want it to. That's the biggest thing I'm finding... I'll probably be kicking my optical drives down one bay so that I can top mount the radiator between the PSU and front of the case, with it venting out the top. That will mean pulling everything from the case in order to cut the vent holes as well as mounting holes for the fans (and radiator) as well as figuring out what type/finish grills I want to use. I might even pick up a roto-zip tool in order to cut the large holes. That way, it will be a cleaner cut and require less filing to finish it off. I want to make this look as professional as possible. That way, if I have a customer want the same thing, I can show them the finished (working) product. That usually closes the deal for me.