Wow, thats a lot of thinking
I suspect this will turn into a discussion about Diesel polution vs Petrol
I'll post my view here and then leave that aspect, and stick to cars and vans...
I have read (on here and elsewhere) how dirty diesel is and how people would not like to live in a poluted UK city, yet in Edinburgh I can see people out running and cycling in this apparently dirty city - if it was so bad then they wouldn't been there doing what they do. Me, I'm fat and unfit but I walk a lot here and I have had Asthma since childhood and it doesn't bother me as much as other factors - the extreme cold recently for example. In fact it bothers me less here than it did before I moved from England. Equally there are people who are more or less floored by particulant emissions. That must be hard for them.
You can add a scrubber to a diesel to remove most if not all of the particulants, a large number of buses have them and a large number do not. Emissions limits are European wide although the quality of air in different cities varies quite a bit as does enforcement. In the UK we have cut back on traffic police (in favour of cameras) so the likelihood of being caught is quite rare, even on main routes or indeed in cities.
I have been in parts of the US where Diesels are rare and the air in those areas (South East) was dominated by the smell given off by catalysed engines being worked hard - that sulphurous type smell. I wonder what that does to people long term.
As for your van, I think you are edging towards keeping it. Thats a valid choice, the money is as well in your wallet.
An Octavia TDi is a good basis for ecomodding. Its basically a VW Golf underneath so you can use all the tips posted for those, and related vehicles - see Vekke's excellent thread on his Cordoba Vario for example. Even the ports and sockets and the underbonnet in the Octavia vs the Golf is more or less identical. The issue you may have is finding a decent one as they are popular taxis when used. If you do go for one, check it over for service history (oil especially) and listen for DMF issues. DMFs are ok but when they go it can be unexpected and expensive.
The Transporter is an excellent basis for an ecomodded practical vehicle though, and will be much less of a compromise than an Astra or an Octavia sized vehicle. If you keep it and mod it then it will be an interesting project to watch, I would subscribe
I have read threads of Aero vs weight in here - search for some of them. Opinions differ but I think its related to the speeds involved. If you go 5-10 MPH less than you do just now you will see a significant saving either way. At higher speeds then the hole you are trying to punch through the air is going to cost you more than weight, at lower speeds or in traffic then getting the weigh moving costs you the most.
Anyway, good luck.