That putty stuffis called "seam sealer" and must be re-applied after welding. You should really brace the original body tub up/down, sideways, and criss-cross so as not to lose original alignment of body. If you are good at oxy/ac welding you could weld the entire replacement piece onto the original after matching up the cut lines. Finish off with proper metal finishing process.
If you are going to just cut out spot welds and replace that is probably the better route especially if you are going to mig it all together. Take copious measurements off original tub and go at it. I would probably start at the "A" pillar then move onto the quarter panel. A bit of a job but can be done. After cutting out the spot welds you may have to do some prying to get the panels to separate. Good luck!
Last edited by fortunateson; 01-11-2013 at 12:13 PM.