I'm no expert but as others have said since you have a 03 TJ you would be better to look at either a Hemi or LS swap. I'm like you and am particular to keeping it Mopar. Also swapping a older year engine into a newer model year vehicle is against emission laws. Yes you might not have testing or inspection where you live but it is still against federal law.
Now on the issue of pilot bearings fitting or not all the folks I have spoken to who have kept their manual over an automatic none have said that they had any trouble with this. Granted it was only 3-4 guys but that speaks well for not having an issue.
https://wranglertjforum.com/threads/hemi-swap-resource-thread.37529/
Now on the issue of pilot bearings fitting or not all the folks I have spoken to who have kept their manual over an automatic none have said that they had any trouble with this. Granted it was only 3-4 guys but that speaks well for not having an issue.
https://wranglertjforum.com/threads/hemi-swap-resource-thread.37529/