In my opinion, unless you want to try and change the lift panels yourself with the roof and vinyl on, is have it done while replacing the vinyl. That's what I did. It surely adds cost but it's incremental and you get it done right and you're done with it. I was extremely happy with ATC who did my Eagle for me. I scheduled it months in advance as I was driving from Idaho. I brought it in late afternoon one day and before I left they already had the roof off. The next day I went back (just before closing) and it was done. Awesome.