Hey G!! sorry to hear about your knee..but glad you are on the mend. I think we got your summer...it was a hot one, but I prefer heat to cold, last winter...was pure hell for me. I've always been allergic, but like wasp stings the poison ivy reaction seems to get worse as I age. I swear all I have to do is look at it wrong..and it includes sumac, poison oak & just about every thing with leaves of three & red stems. being a yardie (new to me term for yard junkie) and living in the woods fighting these things is a neverending job. I must have gotten hold of some roots in one of the flower beds. and with our crazy weather last winter...I even got it in feburary. so whats the deal with the roof? doing a cool roof or something complex? or just having trouble with weather cooperating? sounds like you have perfect weather to get it done this weekend...just be careful up there! do you still have those wonderfully explained igu windows 101 posts from the building forum? I'd like to share them on another forum...maybe in general discussion part of the site as other areas are locked to the publc. I'd really like to get them into the building science forum...but its only for pro members...you wouldn't have an epa card by any chance?? anyway let me know. and again...great to hear from you. take care.

Find the manufacturer's installation directions for whatever the replacement window will be. Here's Andersen's: https://images.homedepot-static.com/catalog/pdfImages/27/273888e4-efab-4463-a51f-20b85cb44957.pdf best way to get water tight seal?? Remove the siding so the window can be properly flashed. $1400 more now but a fraction of what it will cost to replace it (again) later. When this rotted window comes out, be sure you're there to see it and get the forensics of why the installation failed. I'm betting that knowing that will make you feel a lot better about the addt'l expense for removing some siding. Oh, and the upside is that you have cedar so trying to match new siding to old siding shouldn't be a problem.

Would also appreciate some advice. I have a patio door with same transom above. But my door has the seal bulging on the outside (NOT between panes). Can this be easily fixed? Can it be pushed back in? Thanks

Glazing durometer or glazing "gasket". Single pane or double pane window? Regardless, you will need to deglaze the window from the sash/frame, replace the seal, and reinstall the glass.