This unfortunately means I may have to bite the bullet and pay the more expensive contractor in order to make sure my system is not on installed correctly, but designed correctly as well.

This is a segacious statement.

You may also pay an independent certified designer and let the job out to bid.

Well I decided on a route this morning. The company with the high bid will also do a system design and room by room heat calc for about $500. I figure I can go that route, do some of the plumbing myself, and go out to bid for the complicated bits (like the boiler) or anything I decide may be out of my league. I won't have all the cash required for my system for at least a few months, so that means I need to limp my existing system along for the rest of the winter regardless. With that in mind I have until next fall to get everything sorted out.