Heres a few pointers to help you
AFT - sturdy build and very reliable/robust - however if they do go wrong in can be pricey, but there is a lot of info on the forum and factsheets about diy repairs etc
After market roof - pro manual so no working parts to go wrong - cons.....most converters remove the rear air con unit

, and if like us you have passengers then they can cook in warmer weather! Also the roofs are heavy - I got caught out and 'tw@tted' on the noggin when I dropped ours once - fortunately I was moving down at the same time and it only hurt a bit!!!
Out of preference go for the youngest AFT you can and wait to convert. We pondered for about 4 months before deciding on the right conversion to suit us..........glad we did it - as advised on the forum. Also the AFT handles better (suspension setup) than a bongo with an after market roof. When we picked our AFT up we immediately noticed how much better it handled opposed to our previous bongo fitted with an after market roof!
Finally unless you don't mid going slow avoid the 2.0 litre engine - after chatting to 2.0 litre owners at meets - its vastly underpowered to meet the bongos' needs........just my opinion and I know that some others are happy with that engine.
Good luck