Why would the ABS and brake warning lights come on intermittently on a 1995 Trooper LS even after the brakes have been replaced?

Check the brake fluid. If it is ok, take it to the dealer and have the abs codes read.

Additionally, there could be a couple reasons more. For my '95 Trooper, the ABS hydraulic brake cylinder was gradually going out. The ABS brake light would blink on and off going over bumps, then finally the ABS brake light stayed on all together. Two or three years later I had it checked out and the ABS hydraulic cylinder was defective and replaced. My mechanic also told me that the electrical line from the ABS sensor at the differential is known for breaking in a particular location and that also could cause the problem.