Have you tried shifting since replacing the pivot ball?
Make sure you are using the correct lubricant in the transmission. Most T5 transmissions use ATF, NOT Gear oil. That may be why the other trans is burnt up inside. If you use gear oil when ATF is required, you may have problems shifting and you will cause extreme heat in the transmission that will cause the seals, bearings, bushings, etc to fail.
If you need parts, Vintage jeep, I think it is on the web under VJ. Parts are cheap and available. I rebuilt my daughters T5 in her CJ7 for $600. I replaced input and output shafts and third gear along with all new bearings, bushings, seals etc. I met the father and son who own the business, great guys and very helpful, It is located in south Texas.