Definitely not normal, and sounds really bad. It may be that whenever that chip was in there, it did some irreversible damage. But, I have heard similar sounds from guys with loose transmission crossmembers, etc. Go under and check all the bolts, check your radius arm bushings, etc. Things like that could make those clunk noises during shifting. But it shouldnt shift that high on a stock computer, should be 4600, 4700, 4700 (1-2, 2-3, 3-OD) stock, I believe.