We dealt with this same problem (except we had both the captive nuts on the RH side stuffed, so we had to make certain they were going back in the right spot). I will paste our solution below. Note that another (possibly easier) option is to weld in a block of steel into the void, cover with panel steel, then with the subframe mounted mark the location for the hole, then drill tap the hole into the right location. We chose not to do that, we decided to replace the panel sections with the captive nuts welded behind, which means that the placement of the panel is more critical.
Your solution will be much less fiddly than the one below. For you - I would suggest welding a nut to the panel steel patch of the right shape, install the subframe and the patch and tack it in place. Remove subframe and then finish off the welding and painting. We did small tack welds and sprayed with water so as not to damage the paint job with heat.
Morbo28 wrote:
Had the father in law around to sort out the right forward mount for the rear subframe (the two captive nuts in the body were shagged so we had to replace that metal with the captive nuts behind).

We made up a jig to ensue we put the captive nuts in the correct location. We shimmed some spare trunnions with part of some hose clamps so we could fit them onto a 1" metal tube.

Then bolted the spare trunnions up against the trunnions of an assembled subframe.

On a related note there are bigger aluminium trunnions of the same hole dimensions but larger flanges; and also sleeker cast steel versions. The steel ones allow more wiggle room if you need it when installing the subframe to the body. In the pic above the steel one is on the left, bolted to the aluminium one on the right. Also there are pics below - dodgy quality sorry.
Aluminium

Steel

We added washers either side of the jig trunnions.

We tack welded the washers to the tube to lock the trunnions in place without ruining them, to keep the correct dimensions; then offered the jig up to the body.

.

We now had data points to locate the new captive nuts (also used some other measurements). Fast forward three (light) beers and the top captive nut is welded in place. Ran out of time to finish off the bottom one and we didn't want to rush it. So next week we will hopefully have that sorted and finalised so I can then finish the braking system.
Morbo28 wrote:
Got a lot done today.
We welded a plate with a captive nut into position behind the top hole (the original captive nut had twisted and broken free of the body, leaving just the hole in the metal). We did this using the jig, self tapers, bolts and plug welds, tack welds and it was sorted. In the pic below, the ground down area under the top nut is where it was plug welded.

Then we offered up the jig and tacked in place the replacement plate steel with captive nut welded on it to use as the lower mounting point. (don't worry about the wacky angle of the bolt, I had it half removed before I remembered to take a pic)

Removed the jig

You will notice the welds are kind of yucky. It's due to using water to cool each tack weld to ensure the painted panels didn't heat up and stuff the paint up. Also the welds are a little contaminated by the POR paint behind the weld that I used in the cavity while I had rare access to that section. Rest assured we had full penetration and they are strong welds.
More progress

Little more progress

Just like a bloody bought one (well better and stronger actually!)

The subframe even fit it.

We had earlier retapped the threads clean, and pleasingly the jig worked so well that we could do up the copper grease covered bolts using fingers only, then did final torque up with torque wrench.
Not only that...the rear subframe mounts even worked with little fuss. Given we were using a subframe and a shell from different cars, so they had spent their 50 years on the planet apart, we thought we might have to redrill the rear mount holes a little, but no need.

Pleasingly this means that the subframe is (hopefully) in for good.

...