One place to start learning about amps is http://ax84.com/
The BillM Blues Jr. mods are easy to do and highly reccomended. The "basic mods" plus the output transformer make quite a difference. The only scary part is drilling a couple of holes in the PCB. Speaker upgrades also make a big difference - BillM's website has a good summary page. If you're going to do the mods make sure you have a good soldering iron - the Hakko that BillM reccomends is not too expensive and works beautifully.
Beyond that, the BJr is a pretty sweet little amp already and the way it's built doesn't really lend itself to major changes. If what you really want is the "Jerry tone" front end, the path of least resistance is most definitely the SMS. There's lots of info here about building a "Jerry Rig". You'll also want to get the buffer and effects loop into your guitar(s)
There is TONS of info on amp (and pedal) building on the web - just google!