I have had this issue since I have had the CRD, when it rains heavily or I go through a large puddle the ESP BAS, traction control, and ABS light come on. They will stay on for 1-10 mins then disappear. This was only when it rains until a week ago, we have had a ton of rain in SOCAL, now they come on during start up and don't turn off (my ride to work is only 5 miles). I take it something is getting wet and hasn't been able to dry out. Where do I start looking for the issue?

I have a stock 06 limited with EHM and MAF unplugged and 120k with timing belt done at 90K.

Could be a bad ABS wheel speed sensor. Before replacing any of them, check the wiring around them for evidence of rubbing. They will probably set a code, but probably a chassis code which I think most code readers have trouble reading on these.