Thank you, Louavul, for giving him a link to my builders log. I hope it's helpful!
Just to clarify a couple of things. To directly answer your question, Cliff, I had the skin clecoed on all during the trimming and fitting phase of installing the rear window. But I wanted it riveted in place before applying the Sika and putting the window in permanently. If you think about it, it's hard enough to get that skin riveted on. I crawled inside for bucking rivets and had a friend on the outside with the rivet gun. I can't imagine doing all that after the window is in place.
Having said that, I did leave a small number of rivets on the forward "arms" of the skin until later, so I could get the window in place easily with the Sika on it, etc. That worked just fine.
Another builder suggested sanding down the plexi to create a bevel under the skin so you don't need any spacers. That's a great idea. But I didn't do it. For the record, I didn't worry too much about having a certain thickness of Sika under most of the plexi. This is because of my confidence after doing a simple test.
I took a scrap piece of plexi and and a scrap of aluminum, scuffed, cleaned, and prepped them for Sika just like you would for the real installation. Then I went through the installation process as normal, using the cleaner, wait 10 minutes, apply primer. Wait 30 minutes and apply Sika. Put the parts together and let it cure. I waited about a week. This test piece, which I still have, has been subjected to pull tests from everyone interested who wants to check it out. Using all my strength, I can't begin to pull it apart. Nobody else can either. Mind you, this is only about 1" square, and the Sika is less than 1/16" thick. It's really very thin. And here's the real kicker... the Sika products I used on this test were ALL out of date and expired (left over from my tip-up canopy about a year and a half earlier). A couple of them were expired for a long time! This was a huge confidence boost for me. (I used fresh materials on the window, by the way).
I'm not telling anyone to not use any spacers. The recommended 1/8" thickness that the company puts in all their literature and instructions, is designed for marine applications where you can have large, heavy, flat, potentially huge windows on boats. Study the product and the issues and make up your own mind. For me, I'm very confident that my canopy and my window aren't going to fail or come off. Ever. And it looks real nice, to boot. My rear window is flush with the skin all around and it really looks good. There are pictures on my web pages. I'm totally thrilled with how it turned out.
Here's a picture of my test piece:
