With a Bacchetta-style stick bike, the stays can be inline with the main tube. The dropouts should stick down below the line several inches, so that the chain can reach all the gears. The relation between the dropouts, chainstays, and idler will (hopefully, if you do it right) keep the chain from hitting the frame - or the fork. Having the chainstays in line with the main tube will make the seat higher, but will make the bottom bracket lower. Overall the riding position will be less extreme. Rich Pinto of Bacchetta seems to think that 28 degrees is the 'sweet spot' for the seat recline on that style of recumbent. I'd probably aim for that. As for dimensions, print out a pic of a Bacchetta and make a 'blueprint.' If it were me, I'd aim for a 46-47" wheelbase and build it up to my measurements from there.
I don't have much experience with 'tweener bar setups. The easiest way would be to use a pivoting stem such as a Terracycles Glide-Flex stem. The riser will probably be 12-18 inches long, and you can put a standard threadless stem on top. Tweener bars go in front of your knees and pull back along the sides.