I had to search my memory in order to remember roughly how the dyno session went. All the runs were made on the same day; the mapping with the complete system was made first, then the header length runs were made with the same mapping.
I forgot to mention the complete system run was made with the, well, complete system, meaning the headers are 700 mm long. I could not run that version with the bare headers since that would have roasted the rear tire. This means that that run reflects the effects of the shortest headers as well as the collector / silencer.
I would like to repeat this test with a really large-diameter collector I could slip over the header ends on all versions, but I don´t have access to the dyno any more (the operator / friend has gone to another company).
We had some problems with the lambda equipment, but I don´t remember how we eventually did it. We also ran into the dreaded "Nemesis misfire", even if we did not know what it was at the time, so the testing was not quite as systematic as it could have been.
As an interesting side; when we did the header runs I was standing beside the rear wheel (stupidly), holding the exhaust extractor cone against the headers. The pressure on the cone from the exhaust at full throttle and 8000 rpm was amazing, making me understand why the F1 guys are (were) so hot on blown diffusors.
Anyway, here is the same graph, with AFR. Some of the AFR numbers I do not really believe.

With this result in mind, I have settled for 800 mm headers for any 2-1 system I might make in the future.
I do not have any explanation exactly why the full-system graph is so different, but there clearly would be some potential here.
On the stock-with-slip-on vs. 2-1 /PCIII/Open lid comparo, the slip-on is clearly quite lean, I don´t know how much that would affect torque. Maybe Brad could give us a hint here, I don´t know anyone with more Duc mapping experience than him.

The last graph compares a 2-1/PCIII/Open lid Monster run with the Rain bike 800 mm header 2-1 with no-snorkels airbox and some unknown rather rich chip in it. (it has the old 1.5 or 1.6 ECU, so it´s not so easily mapped as the Nemesis). The different runs are just repeat runs to make sure the reults were reasonable; AFR is pretty OK.

I´m also pretty impressed with the stock X collector, as it seems to work very well; I think most of the improvement on a stock bike with a full system is due to lower back pressure. However, they do ground easily and I wanted a 2-1 as tight as possible on the bike along with the tucked-in rear-sets.
Your bike looks very nice with the split headers and megaphone silencers, I think it will work just OK

Nice also to hear you have an XS650. I had one for may years before getting the Monster, 860 cc, Mikuni 36´s, re-profiled cams and (you guessed it) a home-made 2-1. Since this is a Duc forum, send me a mail if there´s anything I can help you with.
And oh yea, Duc forum or not, a nice Commando is a very handsome bike. A pity they are no longer around :'(
(not counting the new version....)