I'm sure it could be done the question would be if you should...right off the bat I'd ask why not a heater core instead, from a wrecker if cheap is important, and if you can drop a few bux the pa heaters are the way to go...the heater core and fan both mounted in a box...as far as plumbing I tried running a "Y" on an auxiliary heater system and found that the fluid would give preferance to one circuit and not flow in the other, so I switched it to a series connection, as in out from the engine to the original heater core, then to the 2nd heater, then back to the engine, and this has worked really well. Are you looking to be warm with the top down? Cuz if normal type heat is what you are hoping to achieve as opposed to the anemic YJ heat, I remember reading an article in JP that said that the tj's heating was far supierior and compatible, i I recall corectly, the swapped a TJ fan and plenum into a YJ with better heat as a result.
Where the purgatory would you fit a heater in the back of a yj anyways?