Sorry for the lonnnngg delay in responding.
I appreciate all of the comments!

Yes it will. Now that the final version of the form is out I think they are just waiting for the instructions to be finalized.

What needs to be synced, in the QuickBooks version at least, are the description and memo fields of the UCOA chart items that state which line of the 990 this account affects. What will also need to be fixed, probably by QuickBooks, is the tax type association of the UCOA items.

This does not take away from the functionality or usefulness of the chart, I think it will be a pain for the folks who fill out hteir own 990's.

If you want to print a copy of the Non-Profit chart of accounts just create a new company file.  To create a new company, you will click on the File tab and click on New Company...Once you open the new company, click on the Lists tab and click on Chart of Accounts or hit Ctrl+A.  In the new company file you will be able to print all of the available accounts.  In the Non-Profit COA the numbers are 5 digits where in the Unified COA there are only four digits.  The Unified COA has specific designations of account types that are based on the lines on the 990 forms.  Also you can import the Unified Chart of Accounts in the Non-Profit version by clicking on the NonProfit tab and scrolling down to where it says import Unified Chart of Accounts.  I suggest printing the COA by opening COA and then click on the file tab and choose to print from there rather than by clicking on the Reports tab and then clicking Lists and printing an account list.  When you print straight from the file tab, the format suggests how you should set up your accounts with sub accounts. 

If you go to www.canonprofits.org you can print their Unified Chart of Accounts because it is cross-referenced to Selected Not-For-Profit Reporting Requirements version 3.0.  In this COA, it shows you the version 3.0 account numbers, the name of accounts, what line item on form 990, what line item on form 990 EZ, OMB A-122 Cost principles and the United Way of America Accounting guide numbers.  Note that there are four GAAP rules-Revenue Recognition Principle which is a requirement by accountants to only record revenue when it is earned;  Matching Principle requires accountants to identify which expenses have helped to generate which revenues and then "match" the expenses against those particular revenues.  "Match" means subtract the expenses from the revenues; Cost Principle  or "Historical Cost Principle" requires that all transactions be recorded at the original (historical) cost.  They must also be stored in the records and presented on the financial statements at the historical cost.  Historical cost is what was paid or charged for something; Reliability Principle requires that accountants record only information into the accounting system which can be verified by objective evidence ( receipts, invoices, canceled checks, bank statements etc...)