You guys are over thinking this. I work at a brewery fab shop full time, and I have "drilled" my fair share of large holes in kegs.
On a hole that size, I would cut it undersized with the plasma cutter, and then use a mandrel grinder to manually bring the hole to size to meet my tube or ferrule. It doesn't take all that long. The downside to using a plasma torch is the large amount of **** it puts into the keg. You will have to clean it out before you weld your tube on. I would remove all pressure from the keg, and add some water so its harder for the dross to stick.
As far as layout, I grind my mating tube or ferrule to fit the surface before the hole is cut, then trace around it. If you don't want to do that, there are other ways, but you have to notch the tube anyway, so I figure that's the most efficient way to do it.
The tricky part is getting a good enough fit so the weld joint can be sanitary.
I have never tried to use a jigsaw, but I suspect that would work fine, it would just take a while and probably eat a few blades. Hole saws work ok up to about 2 inch, then they get a little unruly.
Beer kegs are stainless steel, for those not in the know.