When I have Box A or Box D transactions with a minimal amount of disallowed wash sale losses, I just adjust the cost basis to come out with the right amount.  (For example, $50,000 cost basis and $100 in wash sales; just enter $49,900 for cost basis.  Or should it be $50,100?  I always have to think twice before cutting once.)  I doubt that IRS computer matching is looking at anything but the reported number for gross proceeds, any more than they are looking for fantasy dates on transactions.