Is it throwing a CEL? Stupid question but did you replace the plugs and wires after the fire? Also, check the ground and the harness that connects to the ICM (the part UNDER the coil packs) for damage. Since I don't know the extent of the fire I would visually inspect ALL the harnesses around that area for damage.
As far as the HVAC not selecting where the air goes this may be a vac leak, would may also explain the miss now that I think of it. Check to be sure all of your vac. lines are good and none are cracked/missing/burnt.
