Why are you amending returns for which the statute of limitations on refunds has likely passed?  Is it to pay more tax?  When were the original returns filed?  When were the first amended returns filed?  Have they been processed yet?  Does this involve carrybacks and/or carryovers of NOL's or credits?  

The first thing I would do is wait until the first amended returns were processed, and IRS sent an acknowledgment of the computation.  They may have corrected an error already, like failure to claim 1/2 SE tax.  Use the last IRS computation as the starting point, not the last amended return (which you know is wrong, since you are correcting it).