Check with Hub. I think he has tried all the combinations of engine/header/midpipe connections that are possible and all seem to work with a little pesuasion. Seems like what you would need is a fatter gasket to hook larger 08 midpipe to smaller 06 header.

The can pipes for 06 and 08 are the same ID. The gasket for the stock 06 mid pipes is thicker (1.2mm) than the one for 08. Which means the 06 headder connector nipples are 2.4mm smaller in diameter. Although this is a reduction in size from the 08 there is no cat inside the 06 which I think is more restriction than the slight diameter change.
I had the 06 headders coated before I knew all this or else I probably would have gutted the 08 and coated it. I was thinking about only being down for one day.
Like I've said before, I've been cited here in CA for removing catalytic converters. If I gut mine it would cost a lot more to replace them if some CHP gets a stick up his ass. They let the Hardleys cruise around here with straight pipes.
If my calculations are wrong then I'll probably peddle the 06 ceramics on the site here.