I assume when you say it shifted fine, that was out of the rig, reassembled on the bench?
Sometimes the internals can get bound up, and it takes a bit of force to move everything inside around. The last case I did a 2Low on didn't want to shift easily at all. We ended up using a large 18" crescent wrench to finally get enough leverage to shift through the options. Try spinning the outputs to help synchronize while trying to shift.
Also, make sure you also have the shift linkage installed correctly. There's the linkage tab on the side of the case (held on with 9/16) that can be installed 180 off. Should point up if I remember correctly.
Lastly, being a 97' your case shouldn't have this issue, but sometimes you need to trim 1" off the shift rail. Otherwise it bottoms out on the new tail housing. Pull the plug off the tail housing, and have someone shift while you watch to see if it's making contact.