This may be a stupid question, but wouldn't it be easier and cheaper to just make your MT/LT direct fired, and then add a rake and motor to stir it? You could use the stirring and recirculate during the mash, I would think, to eliminate any scorching issues.
As far as temperature control I think you'll want a PID to eliminate overshoot/undershoot. The PID and temp probe will be cheaper than the Johnson, but you'll have to add an SSR, heatsink, and enclosure. The RIMS tube its self, if you go electric, will cost about $100 with an element, and a 120V element will work fine for maintaining temperatures (I have a 5500W element in my RIMS, but I run it on 120V during the mash, knocking the power down to 1375W). You can build the rest of the control panel for pretty cheap if you don't get elaborate. Really all you need is an on/off switch, PID, SSR w/ heatsink, wires, a power cord, and then the case. I would suspect that by the time you buy the extra vessel, valve and fittings, burner, pilot light setup, controller, solenoid valve, and gas lines/fittings you'd probably be at about a wash, but I have no experience with building an automated gas system.