I've done this restoration many, many times; reverting hacked-up frames from aborted projects. You're doing it in wrong direction and will end up with nothing lining up. Then you'll have to chop off your work and start over again. You need to start from end-result first, then work backwards.
Very first step is to locate tail-light bracket in 3D-space in final location so it will line up with bodywork and fender when everything's completed. You'll need jig to hold tail-light in place while you build everything around it. Luckily, you can use new OEM fender as jig. It has most-important measurement of 4 holes to locate tail-light bracket.
Be sure to add couple washers to simulate bodywork and firmly bolt fender in place so it's rigidly attached. Then use straight-edge strapped to horizontal frame-tube to run its top edge as reference to back. Adjust rear of fender & tail-light bracket vertically so it's in final location. Can use sticks of wood shoved between tyre and fender to maintain vertical alignment.
Then make those little triangular brackets that hold tail-light bracket and fender in place. Bolt all pieces together. When that's done... THEN you fit frame-tubing in place. Don't forget 13.5-degree bend of tubing from frame to tail.
Don't attach new tubing to frame with just butt-welding, it'll break off over time due to vibration and load. You'll want to insert 40mm-long sleeve with same OD as ID of cut-off frame-tubing. Drill hole about 10mm from end of frame-tubing so you can tack-weld sleeve in place. Then you'll really have strong joint with re-attached tubing.