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
Yes, it's very difficult to find a custom ROM that is made specifically for our Japanese EVOs. However, I was able to find the latest RUU (came out less than a month ago?) - software version 2.26.970.1, cook up a custom ROM from it with root and Superuser built in, and apply it to my EVO. As far as I know, I have the latest version possible with full root capabilities. Wimax works as well since I'm using the RUU made for our phones...
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.