I am building an MCR01 and had the same problem. I am fitting a full size second hand transponder. It is all ready to go, but not turned it on yet! It is defiantly the most cost effective way, as the cost of new Mode S will drop by more than the cost of the second hand unit over the time.
One word of advice, if you fit the right transponder, it will use the same size hole and could even use the same tray as its Mode S stable mate. I go this slightly wrong as my tray is not compatible, the man from B-King was economical with the truth!
Rod1