If as some say, in case of problems "One of something equals none" then I'd keep the perfectly servicable and paid-for Kimber and put the $1200 into the Baer.
But then again I've been razzed for being too much of a 'belt and suspenders' kind of guy.
Mr. Yost is said to build a very fine 1911, but so is Les Baer.
A new pistol from Baer would involve some lead time before delivery, as would custom work from Yost. If it was or had to be my only 1911, I'd take how long that currently is running for either into consideration.
A nice used example of either could likely be had in much shorter order, although how directly comparable the features and relative prices might turn out to be could vary greatly.
It seems to me that putting another $1200 of custom work into perfectly good pistol you probably already have some $700-800 in when you can get something so closely equivalent in terms of build quality and features for the same $1200 only makes sense if you think you stand to be able to realize a substantial portion of the total investment if you had to, or what the intangibles of having something "made just for me" are worth to you.
Tough call.