It might work better for the local BBS's to do the calling in to the backbone/HAM BBS's and exchange packets. That way you wouldn't need for the backbone to have designated subs. And if a backbone node went down, the locals could contact the next one on their list, if the first contact failed.
The weak link will be the dialup connections. Too easily traced if a takeover occurred, or phones taken out by EMP.
That is true, but I was thinking more along the lines of a tyrannical government than an EMP. You are probably correct, and I was thinking of HAM operators personally logging into the BBS to upload the files and data they received. Having it done automatically by the BBS computer is definitely an idea though.