Re: putting it back on the wheels etc my feeling would be NO. The doors are your best datum for the door gaps and you’ve set it up for those gaps etc. I would weld it up in the position you locked it into. If you drop it onto the wheels at this stage and it sags you are then going to have to try and straighten a jelly mold by jacking it up in the middle before welding it “straight” - I think you would then be in a world of pain.
That's the point, whatever is done setting gaps on Targa's while the car is elevated, when it is back on its wheels the engine weight will open the gaps at the top of the door and spoil the gaps (i've seen it happen several times). With the car on its wheels and the engine in the car you can set the gaps knowing they won't change. Different ball game with coupe's.
Just trying to be helpful based upon hard learnt experiences of old fatigued Targa shells.