You're talking about three MAJOR mods to a guitar: Replacing the neck (and changing the scale length in the process), moving the pickups and the bridge, and converting it to a hardtail.
What is it about the guitar that you like so much that you're trying to preserve? It seems there isn't going to be much left of the original guitar, which begs the question...
Baritone is a tuning, not a scale length. Lengthening the scale is just a technique used to improve the tonal response as you lower the pitch of the strings. For low tunings, 26 1/4" is not going to add very much tension at all over the PRS's 25" scale... in my opinion, that relatively small amount of change would not be worth the significant degree of guitar surgery you are considering.
If you want a PRS-style baritone hardtail, i'd suggest you get a long-scale neck AND a new body, rather than destroying (and by destroying, i just mean changing irreversibly) your PRS neck and body. If you're tuning down to B (or lower) you might want to consider going with at least a 27" scale.