If they removed the trim and glass and there is a significant (more than a couple of pinholes) amound of rust in the window channel, don't bother putting the vinyl top on as it'll be blistering soon from moisture. The only way to fix it properly is with metal, and if the studs are missing new clips with screws will be needed.

Those prices sound high from that shop (that's front and rear glass R&R, all the metal repair, top install, and trim R&R for $2000-2500?) Does it also include replacement glass if it should break on removal? Good job or not, they really may be trying not to do the job, or to make it well worth their while if they do.