Not sure I follow you on the interior rubber boot issue--03s have the MC in the wheel well below the drivers seat so the brake pedal arm goes thru the floor and is covered by a brush curtain material--no rod????
Ref my earlier posts--the best way to optimize winter dash heating [and summer cooling] is to put the dash selector on "Max A/C" and turn the heater select to full heat side, then turn the fan up. This blocks outside air from coming in, and allows the dash fan to overcome the partial vacuum that forms in the front cab/genset compartment at hi-way speed. Yes this does cause the AC compressor to run so if you are going to be in cold weather for an extended period, you can disconnect the compressor clutch wire on the A/C to prevent compressor run while in this configuration.
PS--If foot warmth is still an issue, you can physically connect splice/tee the floor vents to the ducts coming from the the upper vents so while you are in the "Max A/C" config, heat is diverted from the upper vents.......
2003 40' MDTS
Garden Ridge, Texas