I just purchased a 1998 Isuzu Rodeo with 155,000 miles. The truck is in excellent shape. However, it is making some weird and annoying clunking noises when shifting to 2nd or 3rd gear. It appears to be worst in the morning time.

Check the tranny fluid level.

If you don't know the history of maintaince, I would suggest dropping the tranny pan, change the filter and and put in some new tranny fluid (this method will change out about 40% of the fluid, which is ok on a high mileage tranny).

Hard, clunky shifts could also be a bad transmission range sensor. Very common problem on the 4L30E trans. Try a search for range sensor.
G/luck
Joel