I feel your pain, man. Some of it will go away, but a bent isn't an upright. You're probably not going to regain those rocket starts.

The wobbles will go away, start-ups will get better, and the speed will come up. I never did pass cars at lights; it's unsafe at best and illegal in most places, too. The shifting problem should be looked at; a long chain is no excuse for poor shifting.

Your 1000-mile estimate might not be off too far; it took me a good part of a season to bring my recumbent speeds up to the level I'd been on my upright. But without a fairing or some other aerodynamic aids, I think the hull speed on a Django is going to be no better than your road bike -- 17-18 average mph might be about what you can expect. OTOH, that might not be bad compared to what you 'd get from raising the bars on your road bike to a comfortable level.

I never liked the Burley seats. I think they're too upright to be that hard. Maybe it'd be better if you put an inch or two of upholstery foam on it and covered it with a lycra cover. In other words, made it more like a RANS combination seat. Plus, if you're having problems with recumbent butt, recline the seat more. The idea is to distribute some of your weight to your back. That'll help with the butt as well as with cruising speed.