Sounds like you made a classic mistake. You didn't deburr the shift shaft before you put the new NSBU on. There will be a flat spot on the end of the shaft where the shift arm hooks up, and if you don't deburr it you WILL gouge the inside of the new NSBU and have the problem you describe. As for differences, if you go to GM they will sell you the new style trans for an 01-early 03 truck. It plugs right in, and with the adapter fittings the cooler lines hook right up.