Whuntmore, get your metal prep and painting done first. Then after it has had a chance to cure, you can start on the prep for the new windshield. There should be some rubber spacers that you had to cut out of the old urethane. If they are still useable, then put a dab of new urethane on the bottoms of them and stick them on in roughly the same spot that they came out of. Let the urethane set up for a bit so that they do not slide around while you try to put the new windshield in. Next, put a bead of urethane around the frame that is slightly higher than the rubber spacers. Make sure to cover the top of the spacers as well as around the perimiter of them. That is the most common area for a new windshield to leak. After that, get a friend to help you lower the new windshield into place, this is a great time to have some rubber gloves on because that urethane will get everywhere and it will not come off your hands for a really long time! After the windshield is in place, carefully "thump" it with the palm of your hand all the way around the edges. This will help to seat it in the urethane properly. Do not "thump" it too hard though or you will risk cracking it. Once it is in, then you will want to clean up the stray urethane that will undoubtedly get all over the place. Mineral spirits or goof off works well for this but watch out for paint that has not had enough time to cure! you will damage that nice glossy look with caustic chemicals. Next is to get the trim back on. Someone chime in here because I cannot remember, but I think that the Eagle has the clips that need to be set into the urethane to hold them in. If this is the case, then dab a little urethane on the end of each clip and press it into the window channel. This is what holds it in for all those high speed maneuvers.
After you have all the trim pieces aligned, make sure to use some masking tape to hold them tight against the windshield and body. Be generous with the tape, this will assure that the trim pieces sit flat.
Some added notes:
Roll down the windows slightly before you start and keep them down until the urethane has had a chance to cure. if not, then you run the risk of blowing out the seal that you just worked so hard to attain.
If you lost the rubber spacers, check with a local body shop.
Take your time in setting up everything you need before you start. After you get going, there is no stopping.
You can take the time to mask off around the windshield with tape and newspaper if you want, this will pay off in the long run with trying to track down all the nasty black goo that is left behind.
Wear clothes that you don't care about and have lots of rags within reach.
Please add more if anyone can think of it.
Dustin