This is where pictures really help so we can see what you are up against and what you are describing to help give better ways to address the problem.
If you need help posting a pic, let us know, we can help.
Now to your issue. I "think" I understand what you are talking about. Is this the front of the camper window under the rock guard (non opening window) or a window on the side of the coach? When you said the glass was too short my mind went to the very front window under the rock guard. We have had some folks with issues on them leaking around the glass seal. I "think" 2006 was the year Sunline stopped putting the front windows in due to too many issues.
But to your soft spot regardless which window it is. There is a way to check if that soft spot is wet wood.
Ideally you have a helper. Have the helper be outside and hold the window in towards the camper.
Go inside and remove the metal flange that holds the window in. There are many square bit screws all the way around. That metal flange holds the window into the camper. So do not push on the window. The putty tape on the outside will still have the window stuck on but depending on the condition of the putty tape it may not be holding by much.
Then once that flange is off you can see the wood. Get a flash light and really look and sniff. Yes sniff. If it smells wet and musty, you well may have rot going on. Now don't fear, there has been many thru this deal before. If your handy with wood working you can fix everything. But first need to know some of what you are up against.
Here are some pics of the window flange I am referring to and what it looks like inside with it off. You can see the wood studs. This is not a wet issue why I had this off it was to insulate the air space.
The entire flange off
You may be fighting 2 problems. The glass issue you already had fixed and a leak in the putty tape sealing the window flange to the camper. Doing a reseal of the window to the camper is straight forward and we can show you how to do that too but we will recommend using butyl rubber sealing tape in place of the putty tape. But first lets see you the issue is
Good luck and hope this helps
Current Sunlines: 2004 T310SR, 2004 T1950, 2004 T2475, 2007 T2499, 2004 T317SR
Prior Sunlines: 2004 T2499 - Fern Blue
2005 Ford F350 Lariat, 6.8L V10 W/ 4.10 rear axle, CC, Short Bed, SRW. Reese HP trunnion bar hitch W/ HP DC
Google Custom Search For Sunline Owners Club