I think there a couple of important issues to consider here, as usual they are competing difficulties. First, as you have touched upon, is the original pivot point in relation to the engine. The ideal pivot would be concentric with the output shaft/countershaft sprocket. That of course is to make life easy for the drive chain. This is very complex/expensive to implement manufacturing wise, so engineers place the pivot as close as practical that center. There is an additional strong benefit to having the pivot actually be part of the engine case, as all the loads can pass directly (more or less) into the swing arm and not have the engine mounts/frame work as a middleman. While moving the pivot back behind the sprocket center is undesirable, it's not too bad if it is very close and the arc the arm passes through is small, which brings up the second point. Moving the pivot further back, say where the original frames swing arm pivot is, places it quite a ways behind the sprocket, and the resulting change in chain tension as the suspension works becomes unacceptable.
Moving the existing frame pivot forward also creates some issues. If you move it to align with the engine pivot, you will be rather a long distance away from the existing frame. That places the loads input from the swingarm on the end of a much longer lever and will likely add flexibility to the system, though how much and how real world important is hard to tell. Increased likelyhood of vibration fatigue cracking also becomes something to consider. Swing arm pivots are placed as close as possible to the frame structure for a reason - look at the originals. Certainly relocating so far away will add some weight, but being coincident with the engine pivot would definitely be a plus. Personally, I would have the aesthetics in mind as well - I think a lot of flat frame real estate in this area is not too desirable.
Discounting other issues with moving the engine back (fitment, weight distribution), you would ideally align the engine pivot with the frame pivot and alter the swing arm to fit in between. Looks like you have spent some time figuring out where it is now so moving it may not be practical. Also, looks like there is enough distance here to consider the wheelbase and tire clearance with potentially moving the swing arm so far forward.
If that is the case, I think the job will not require any sort of major frame jig. Get the engine aligned exactly where you want it and mount it so you can get the swing arm fitted to it. I've made temporary mounts on occasion. Probably less trouble than you expect to fit the swingarm. The thing to remember here is that swing arm rotates on a fixed, solid, structural frame element comprised of the through bolt, inner bearing races (or bushings), any sleeves or spacers (including the engine) and the two frame elements. The swing arm is captured by these components and shimmed or otherwise fitted to eliminate any play. With this in mind, and with the swing arm fitted to the engine and the engine in place, you only will need to build structure between the new frame mount and the existing frame. I would think you could get this all mocked up with the existing swing arm mounts still in place, and use them as a benchmark to ensure all the new work is properly aligned. Once you are certain everything is lined up, you can remove all of the existing swing arm mountings and simply tack weld new structure in its place. Take the engine back out, put the pivot bolt and bushings, sleeves etc back in and tighten it down. In your case, you probably will have to make a long spacer to replicate the engine, any spacers and bearings in the actual assembly. With a bit of care you should be able to finish weld everything with out too much trouble. There will be some distortion, but no more than you would suffer with a complete frame jig.