Update: I haven't worked on this in many moons and it has ceased to work. Here is a currently working MBTA map.
Ok, so it's not that useful right now, since it only covers a small part of Cambridge at one zoom level. And since I don't really have the time to keep working on it right now, I'll post what I've got so anyone else can continue.
The 4 downtown maps work best when rasterized to a 1710px wide canvas (before cropping) to create the tiles for zoom=2. I experimented with different sizes and even figured out the pixel/mile ratio (more below), but that didn't help.
The PDFs are nice enough that it should be possible to create tiles for multiple zoom levels.
The MBTA also has a nice Trip Planner that could potentially be scraped to provide transfers on the sidebar (where driving directions would usually be placed). It appears to use lat/lon pairs internally, which is helpful.