I understand the pain you are going to. I quit my first estimating job for the same reason.
I was working for small custom home builder company, The owner/CEO was trying to "organize" the company and change the estimates and specs formats from the company "own particular format" to an industry standard format (MF 2004 or Uniformat).
The owner and the computer geek decided to go with Master format for the parts book and uniformat for the estimate WBS. I admit the owner did not know what he was getting into.
When the first estimates in the new format came out, he did not like it because he could not see the cost the way he was used to see it. Therefore, the WBS was changing as per his request from one estimate to the next.
It was really fustrating for me because regardless the WBS I had to make sure everything was acounted for.
On my third job, I'm having similar challenges in which the senior estimator wants to use MF but the general construction manager wants to keep it the way it is (we have our own particular WBS).
My opinion is, prior to changing the system everybody involved in creating, reviewing and using the estimates should be trainned and explained the importance of knowing and understanding the WBS (that include: owners, managers estimators, accountants, sales and site superintendants). Many people agree with changing it but do not give the importance of actually knowing the new system and seeing the future challenges.