Hey VL,
Im not sure, but from the pictures it looks like you made another mistake that I also did when installing my acrylic windows: I pushed the windows up tight against the tank and squeezed alot of the silicone out. I ended up with only about 1/16" of sealant between the tank and the wood. After I installed my windows I found a detailed write up by Anythingfish about how he did his windows. Evidently, one should use some spacers between the acrylic and tank frame to ensure that the windows are not pushed up too tight against the tank. I think it is supposed to be like 3/16" or 1/4" gap (filled with sealant, of course) between the acrylic and the tank. When it is dry, you have a nice, thick, gasket between the windows and tank. I think the function is that as the tank is filled, the water pressure compresses the sealant gasket that you have made and improves the seal.
How much do you want for the windshield removal kit?
Thanks for the pics. Keep up the good work.