What you plan to do with the build should give insight on cutting or keeping.. What style are you going for? If you want a long stretched "digger" or a goose-neck, the factory neck doesn't really flow with that style.. so I'd say fab a frame and keep the OG one intact.
If you want a stock rake short hardtail, cut the frame at the downtubes and the backbone, (Keep the rear portion to graft back together when you want to "restore" the frame) graft on the rear of your design and build from there.
If you really don't care about any originality, just get the saws and welder fired up..
Just a thought.