The temperatures should be fairly similar. Is this a new problem, or has there been a difference in temps since the new pumps and H/E cleaning? Sounds like there is significantly more water flowing through the stbd exhaust riser than the port one. The question is why? I would be inclined to check the raw water pump impellers first. Are the sea strainers and through-hulls clear?
If all else fails, read the instructions
If it ain't broke, don't fix it