Hi.
For me it's primarily about panel damping as it's the primary cause of noise in vehicles. I was surprised how little damping the Bongo has. As you say, it started life as an MPV.
The main driver at the moment for giving the roof attention is acorns (no, I haven't taken leave of my senses

). We have loads of oaks round our way and the first time one dinged off the roof as we were going along I thought we had been shot at! Every one in the van jumped and say "What was that!". Amazingly loud. Even rain is pretty noisy, especially if you are parked under trees. So deadening should help a lot. Thermal insulation is also a goal.
The front section of the headlining has a dense foam layer forming it's structure, but that will not stop the roof panel vibrating as it barely touches it. The rear headlining (at least on mine) has no foam layer and has nothing but a single thin sheet of old school yellow upholstery foam literally just laying on top of it. If I move the headlining up and down it wafts about! There should be gains to be had by damping these panels. There will certainly be thermal advantage in insulating the back section of the roof with neoprene over the panel damping.
There is a small amount of factory fit bitumen applied to the foot wells and the back of the dog house, but I'm not sure how effective it is after 12 years of being baked. All the engine covers have is a thin sheet of fibreglass material hooked on. That certainly won't stop any panel vibration noise. You get major noise reduction damping this area.
The doors have no sound damping at all, but there is sufficient access and space to fit it. I've got 4 large sized PeaceMats fitted and 2 small with 3mm neoprene over the top. I recommend gloves though to prevent scrapes! I would agree that filling the void with loft insulation or wool would cause damp problems. Ditto with the side panels. Peacemat and neoprene seems to do the job and shouldn't cause moisture build up issues.
As to the floor, don't get me started

The carpet was obviously removed when the conversion was done and the company who did it didn't bother putting down any sound proofing. So the majority of the noise I have left is from the exhaust system running under the floor. The floor also gets quite warm after a journey. Unfortunately, I'm going to have to take out the interior if I want to fit sound deadening to the floor
Anyway, this all keeps me occupied and I'm pleased with the results so far. Discovered a couple of surface rust patches on the inside of the roof panels in the process. Learning lots about how the vehicle is put together as well
There must be things you can do to the suspension. Adjustable shocks for example?