After asking lots of questions and getting lots of useful advice from forum members, I've got some ideas to share on roofbars which might be useful to any paddling bongo owners out there.
I discovered that the old Paddy Hopkirk roofbars I had for my previous car fit well into the threaded holes in the AFT, with only a minor modification to drill out the existing holes in the roofbar feet to allow the M8 bolts to fit. These bars are more or less the same as older Thule/Mount Blanc types or cheaper Halfords ones, so it's worth having a look if you have any of these lying around (I seem to collect old roofbars from previous cars)!
However with the roof being so high on the bongo, we weren't sure how we were going to be able to lift our heavy canoe onto the roof. Karitek do a great system, but it isn't cheap. I thought a roller at the back would be a simple solution, but without fixing points for a bar at the back of the AFT that looked tricky - this system seemed like a good idea but none of the ones available were quite the right width for my bars or a canoe, and didn't extend far enough back. However it gave me an idea for a way to make my own.
My roofbars came with a roofrack to carry luggage, which we'd never used. You can pick these up cheaply on ebay if you don't have one to go with your bars, 102U is the produce code for one to match the 114cm wide roofbars. Firstly I dismantled it, and discovered that at some point we had lost the special bolts which connect the rack to the bars. No matter, a few cheap L-shaped brackets from B&Q did the job instead; I drilled out the holes in the brackets to accommodate the bolts (M6 I think) which attach the bars to the roofbar feet, and because the feet are right out to the edge of the 114cm bars on the Bongo, you can sit the bracket underneath the threaded plate inside the roofbar, with the bolt gong through the whole assembly, and once you tighten it all down you've got a bracket sticking out of each end of the roofbar to attach the side parts of the roofrack to.
It's about 63cm from the back of the AFT to the rear roofbar mounting bolt, so to get the roller at the very back of the AFT, attach the new brackets you've fitted into the holes in the side plates of the roofrack that are a quarter of the way along their length. I found it easiest to reverse them so the writing faces in the way and the metal lip out the way, and also upside down - you'll see why later. The roofrack comes with three crossbars; I mounted two at the front (this helps give the whole thing a bit of rigidity, and protects the sunroof slightly to avoid a boat getting dropped on it). The third one goes at the very back, in the lower of the two holes, and to make this into a roller I slid this inside a bit of PVC piping (30mm would be ideal, 32mm was the closest I could find). Before fitting it, get another two small brackets, and two of the rubber doorstops you screw into floors to stop doors hitting walls; drill the bracket to accommodate the M6 bolts, then attach the bracket inside the lower mounting point for the rear crossbar. Another few bolts will attach the doorstops into the horizontal parts of the bracket - if you have them facing out the way the doorstops should sit nicely in the AFT gutter.
That should be it! When lifting on a canoe or kayak, leave the rear end on the ground to the rear of the bongo, and lift the front onto the roller bar. Then you can pick up the rear end and roll it forward onto the roofbars. The side parts of the roofrack stick up at the rear meaning the canoe can't slide off either side as you roll it on or off. The weight of the boat sits on the roller and doorstops while you use it, but because it is lower down than the roofbars, there is no weight on it once the boat is on the roofbars, so you won't damage it or the roof when tightening the straps down, even with a canoe like mine where the gunnels are higher at each end than in the middle. It's a doddle to load and unload it this way, even with one person, and I'd imagine this system would work on other vans or estate cars too. Hope this all makes sense, the pictures probably show it better than my words!
Happy paddling,
Jamie
My tip is DON'T GO ON THE RIVER WHEN I'M FISHING! 
