I was doing the import export thing with Thunderbird. But if it's the same version of TB on both ends it's just simpler to copy the Mail folder to the new location. If drive letters and all that are the same that's all you need to do. If you have any TB extensions such as AutoCopy or some of the folder managers or custom buttons then you may have to use an extension saver/backer upper.
edit: in fact you may be able to get away with just copying the whole "profiles" folder from one install to the other. The time to try it is before you do any customization on the new install. Copy the new Profiles folder to a temp folder in case the new install gets totally hosed you can just copy it back.
MozBackup does work. Where you can run into problems is if you accidentally try to retore and old version backup onto a newer version install. Got into that nightmare with Firefox. It's easier just to copy the whole settings/profile folder someplace, like an external drive.