My old '97 AT had a similar problem. The shifts were kinda hard and had extended shift times. This is what I found but I never got around to testing anything.
Your transmission should have a dipstick somewhere on top. I believe it is under the intake tubing and has an orange handle, it's not the easiest thing to find and it is pretty short. The dipstick can be sucked into the trans on rare occasions. Do not try and remove the dipstick if this has happened. Make sure the fluid is not extremely dark or that it smells burnt. The ATF is a red color when new and should not be super dark when checked. The fluid also smells pretty horrid out of the bottle, burnt ass is a fairly accurate description.
I've done research before and the best fix (aside from replacing the trans) is flushing the trans fluid 3 times. I have never done it but I've found several people that all claim little to no improvement from 1 or 2 flushes but a fairly large improvement in shifts after the 3rd flush.
Try to keep rpms down between 2nd and 3rd. Keeping strain off of the trans will help keep it working longer. If there are any circumstances that cause a hard shift or a large jolt, definitely try to avoid those circumstances.
