worked on my mendel over the last several days, and installed different firmware. using http://github.com/mccoyn/reprap-firmware-fork i believe. with some minor modifications for the pin outs im using. I am still having some issues with movement but the motors are stepping now at least for the most part :)
The thermister table appears to be off but that is easily fixed. not sure yet if there is anything else missing from that firmware branch but at least it communicates with the reprap software without locking up.