On my '99 Limited with the automatic temperature controls, it blows about 1/2 the pressure out the driver side vents than it does the passenger side (the driver side middle vent under the radio and the driver side vent by the door). It does this in heat and AC.
The biggest part runs inside the HVAC housing. You can only split that one when its out of the jeep, but to do that, you would have to remove the whole dash.
Are you sure that both air outlets are functioning properly and open completely?
JEEP Grand Cherokee 4.7 Lmtd 2004
HID 8000K in low and fog / Quad Squad member
KYB Gas-a-Just shocks / Pirelli Scorpion ATR 245/65/17 - Transgo reprogramming shiftkit.