I've never heard your arguments but they are intriguing (in a woulda coulda shoulda sort of way).
The ted williams tunnel alignment argument I get, but I think the reality of that alignment is that it would either have to go under the blue line for half a mile or so, or surface, the latter of which would have just traded the balkanization of the North End in for cutting off Maverick Hill and Jeffries Point. By pushing it east it adds 2 minutes for drivers and keeps eastie consolidated. If your alignment were indeed being proposed, I would also argue against the Seaport connector and instead get traffic going there to surface at summer street and hang a right there
But I'm super interested to hear you idea about sumner callahan.... how about closing one, putting in an LRT line, walking and cycling lanes and rent vendor space out? Take the remaining tunnel and make one way--inbound in the am, outbound in the pm?