While I have a different rig, I had the same problem.
I had a professional glass installer do a seal replacement for me last year. He works for glass companies and had experience with MH windshields.
I bought the rubber seal (it was all one piece for both sides) off the internet and he and a helper installed it. They would not guarantee not too break the glass (don't think anyone would except maybe warranty work).
They carefully took the glass and old seal out and then cleaned and prepped for the new seal and old glass. It took about 2.5 hours and it was all back in. It is working fine and they did use a sealer around all the rubber and glass after installing.
John & Deanie, Corky and Benji (best buddies)
2001 National Marlin 390 DP
"Try to live up to your dog's opinion of you."