I've chopped the roof on my car, using Archie's Kit (w/glass side windows). I haven't completely finished ALL the mods I'm doing but the Chop is Done... Removing the rear clip is pretty straight forward when you get going. Only drilling I remember was a rivet or two on the Side Quarter panels, the rest is just un-bolting. The front clip was more difficult due to the adhesive and trying not to break the panel when separating it from the chassis. I paid a lot of attention to detail and quality in my build and It has turned out, so far, really nice.
"I don't know about cutting the sun roof area (if you have a sun roof) to save trimming the forward roof clip a little. Seems like you'd be opening a whole can of worms trying to get the sun roof back in..."
There are a lot of details to doing a chop that I haven't seen much posted about, Modifying Door glass stops, Door Track & Seal Mods, Rear Quarter window trim, headliner panel ect.
Are you doing a Kit from Archie or a Home Build ?I have taken ALOT of photos of the build process on my car but haven't posted them anywhere. So if I can be of help
let me know.

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88 GT
Choptop, Vertical Door Hinges
Lowered Suspension w/ 13" Brake Disk
CarPC - WinXP Pro (GT Sport Edition)
+ a lot more.....