Need some file upgrade help/suggestions

We upgraded from 2010 SP4 to 2012 SP4 a cpl of weekends ago and plan on going to SW2013 first qtr next year.

I will try and answer the common questions that pop up ahead of time.

1. Why are you converting all files. Answer: Our larger assemblies are opening slower than they were in SW2010
2. Why not convert as needed?  Answer:  The majority of sub assemblies and parts that our assemblies and drawings reference will probably never change so why would the user open a top level assembly and check thousands of parts and assemblies out (which may or may not be the current version) for the sake of converting.  With the amount of users we have files would be checked out numerous times....

We have 77930 part files, 29022, assemblies, and 65,322 drawings.  I do not plan on doing the drawings since they will be converted when the user checks them out and saves them.  The weekend we went live I converted 59,000 part files in the vault and have 19,000 to go.  In addition we have 28,000 assemblies that still need to be converted.

I am looking at having 20 or so computers upgrading the rest of these files starting Wednesday evening throughout the weekend.  We will start on the rest of the parts.  The issue/concern I have is the way the upgrade tool works.  It appears that the tool is not set up to look to see if the file is in the current version until after it checks them all out.  That means it will need do a check-out on all 77,930 parts which only ~19,000 files need to be converted.  The three issues I have with this are Wasted Time, Un-needed stress on the system, and baby sitting. If I have 19,000 parts split between 20 computers that is 950 files per machine.  Lets say just one of those stop and is not able to pick where it left off for whatever reason.  Now I have 950 files checked out that I manually have to deal with.  The real bummer of this is that there is the potential that these 950 files were already converted on go-live weekend.

I am not as much worried about parts as I am with assemblies seen as they could potentially have some references pointing outside the vault and potential cyclical references which in the past have caused issues with the upgrade tool.

One last thing is if these machines are not done crunching by the end of the weekend how can somehow I stop them and have them pick up were the left off?  Our folder structure does not lend well to select a single folder at a time seen as though we have thousands if not hundreds of thousands of folders.  We tried to keep to 1000 - 2000 files per folder.

I know which files need ot be upgraded, is there away to feed the upgrade tool a list of files to do verses a folder and or all sub folders? 

Any suggestions or tips would be appreciated.  Thanks, Bill