I've also found that the amount of heat that gets sent to the floor area in these cars to be pretty sad. There are a few things that you can check to be certain your'* is working properly. First is to check your cabin air filter. If that starts to get clogged, it will restrict the air flow.
The hush panels under the dash also serve as ducts for the heat. If those were pulled down to work on the intermediate shaft, they may not have been reinstalled properly. Pull especially the driver'* side down to check.
While you have that down, check to see if the boot covering the intermediate shaft has been cut. If so, has it been taped back up? Sometimes they don't tape it back up, and cold air enters that way.
Black 2000 SSEi, Silverstar Headlights, Angel Eyes fogs, 3rd brake light overlay, hi-flo cat, drilled 180 degree thermostat, Intense FWI, PCM, shift kit, and 3.4 Pulley. Solid front mount.