Yeah, it did go pretty quick. I believe the best decision I made was to abandon the 99 model donor I had picked up for $125, sold my 2007 KLX300r and bought a 2005 KX-125 for $2,100 that had literally barely been ridden. I sold the kx motor for $930.
This was our first ever project of this type. I'm no mechanic and I believe just about anyone can do this.
I got all my information to do the build on KDXrider.net (i hope I can say that here?) They have a KDX-MX Hybrid forum. GREAT info.
Again my recommendation is to use the best 2003-2005 KX you can find.