versions of the story
The scroll is indeed in private hands (Jim Irsay), but is beginning a traveling tour of exhibitions. The first stop was last year at the Lilly Library in Bloomington, Indiana. It is now on display in Orlando as has been mentioned. I had a chance to examine the scroll closely while it was in Bloomington and I do not recall any mention of Shephard. But, yes, there are large portions of the scroll that were cut from publication, so it is possible it is there.
According to the post-auction catalog from Christies, the versions of OTR are as such:
1. typescript scroll (owned by Irsay)
2. typescript (codex-form) prepared from the preceeding for submission to publishers. Reportedly part of Kerouac archives.
3. typescript (codex-form) prepared for submission to publishers, with markings of Viking editors. Reportedly part of the Kerouac archive.
The Kerouac archive is now (or at least partially) at the NY Public Library. I'm not sure what the status of accessability is for it, but those typescripts are probably your best bet on answering your question.