The version with seats already was type approved for the UK as a passenger carrier and would be taxed as a diesel passenger car if it wasn't for you qualifying for the disabled bracket due to your daughter. The version without was type approved as a PLG vehicle and would not pay based on CO2. What is relevant to tax class is the information Mercedes fed the DVLA from the factory, not what you use the vehicle as now or what it looks like now.
The odds are very good that your panel van 'flavour' was built to the N1 standard of panel vans/PLG vehicles. The window van 'flavour' would have been build to M1 passenger carrier standard. The two likely would not look identical, as you admit seats were added to the rear by the converter, rather than the rear most seats being removed by them. This is why your V5 says it has three seats when it has six. It left factory with 3. Chances are good you could have ordered a window van from Mercedes with the rearmost row of seats deleted and gotten a few hundred off the price for doing so, but that's beside the fact.
You can ask the converters if they should have had the vehicle re-type approved for carrying passengers after their conversion was done because you understood you had a passenger carrier not a goods vehicle. Unfortuneately, to Mercedes, that van will still look like a goods van in their systems so they likely can't help you, and the DVLA will ask you to get a letter from the maker to state the vehicle was misclassified by the factory. Its just that from their point of view, its not misclassified. If you got on well with the converters, call them and explain the situation. Maybe they can submit something to indicate what they have done in the conversion has changed the purpose of the vehicle? I've been lead to believe that M1 vehicles are safer in the rear as they're intended to have people in instead of tools, but that would again be something to do more research into.
Otherwise you'll just have to keep to lower speed limits and live and learn. At the end of the day, even if you were allowed to do 70mph, you were still speeding. Certianly by a lot less if you were classed as a car than a van though.