Before you start welding, I have some suggestions for you to consider.
First off since this is new to you I would cut the patch panel a little shorter on the rear side just in case you screw it up, then I'm assuming that you can get another patch panel if you need to.
Make sure the 1/4 panel is as straight and smooth as you can get it beyond the patch area---as mentioned.
On older cars with a lot of door adjustment, it would be wise to get the door adjusted the way you want it before cutting anything on the car.
Cut the front flange, the bottom flange, and top flange off the old 1/4 panel to allow the patch panel to seat properly before making your seam cut. It may even need a little work to make it fit right.
For the cut, I would use an electric body saw. I have had a couple of these in the link and they have worked flawlessly for years of intermittent use.
http://www.harborfreight.com/electric-b ... 65766.htmlIf you watch the video in the link you can see that the cut is only as wide as the blade. It only cuts with the leading edge, but the cut off wheel has a large cutting edge (the whole disc) so if you don't hold it absolutely straight then the rear edge will make the gap bigger. Its even difficult to make a small slit the same size as the cut off wheel.
Personally, I prefer to scribe and cut on the line, but it does take some tin snips, more time, and a file to get it right.
To secure the patch panel at the weld seam, you could get a strip of copper sheet for backing and attach it to the old section with screws allowing half the width to extend forward, and after you lay the patch on it then drill and screw it also. You can probably clamp the patch panel at the bottom and top, then drill and screw at the door jam. When you finish welding you should be able to get the copper strip out the window opening, then just weld up the screw holes.
Put tack welds top, bottom, and middle of the seam, then keep putting them half way inbetween until they are all one inch apart. Allow the welds to cool naturally without compressed air or anything else that might speed it up and jump around with your weld tacks.
Good luck