based on what my local skylight company quoted - something like $1500 or $1800? i can't remember - the tax credit and rebate still don't make it quite affordable... i guess the question is: would there really be a noticeable difference between the low-e and the acrylic - significant enough to make a replacement of a new skylight worthwhile for the first price quoted? i know that's a subjective question since $800 means different things to different people - but i guess another way to ask the question is: do you really believe in the low-e glass and think i'll really feel the difference? i should say that said skylight is in my studio workspace/converted 2 car garage which i work in every day - the ceiling isn't insulated and it has a metal garage door so i'm battling a lot of heat sources....and it's hard to tell how much of it is coming from the skylight per se - but it's one thing i can change so wondering if it's a good idea....

If the flashing on the existing curb was fine, you would not want to disturb it as a normal procedural process (assuming the curb size is correct for the new unit). Every home is different. I suggest you get a relative humidity gauge and see where your levels are and what the levels are inside the skylight shaft. That will take all the guess work out of the questions you are having. Amazon has them and I have used this one: https://www.amazon.com/RockyMars-Temperature-Humidity-Monitor-Hygrometer/dp/B01M3Q2T21/ref=sr_1_12?s=home-garden&ie=UTF8&qid=1500913462&sr=1-12&keywords=humidity+gauge  As a general observation, the tighter homes and installations will have more issues with humidity. If you neighbor's homes are getting more unintentional ventilation (i.e. doors opening and closing), the humidity level could still be higher in your home.

Thank you for your response, but we already know that the skylight is a problem with early morning light for the bedroom that is just a couple feet from it. The door to the bedroom is almost adjacent to the skylight in the hall, and the bed is right next to the door (it's a small bedroom). At 5-6 am May-August, the light comes right into the sleeper's eyes, around the door edges. The skylight is old and somewhat clouded and stained. I expect the new clear glass skylight to be even brighter. The problem is mostly in the summer. I think my question is whether the blind's stackback when fully open and/or the carriage that holds it will be obtrusive on a 36x36 skylight, so because of that it's not a good choice. Or does the blind fold up to such a small width, that it's not a big deal.

I would get an architect involved. Velux designers will help with the skylite but they are not qualified and will not get involved in the roof structure planning, nor should they. This goes for anywhere just not the state of California.