When I gutted my interior, the whole kit & kaboodle came out as more or less one piece, though the heater core and a/c evaporator came out as separate pieces. I suppose you could put them back in after you're done, but its such a PITA to rip all this stuff out, I would just plan on bypassing those pieces and calling it good.
Dumb question - are we talking about the same blower assembly that you tear out in the engine compartment? I know that there are some other pieces under the dashboard for air distribution, but I remember the main blower being the only substantial fan.
Not sure about making things fit, I've never seen the innards of a car w/ a knee bar. Hope my ramblings are helpful, in any case.