I rooted once before and backed up the WiMAX partition like you say. However I couldn't get a connection which seemed to be a common issue with those rooting the Japanese version of the evo, as most roms use sprints' base whereas here we have au which uses a different software version and whatnot. Did you manage to flash without any problems to your WiMAX here in Japan?
Evo WiMAX Japan
My next step is to build another custom ROM, take out bloatware, and maybe learn how to tweak it a little bit...but, I'm very much a beginner at ROM cooking...so it will take some time.