If you're determined to do it, I'd check out left luggage options at the London rail terminus you'll use to get to/from Duxford (Liverpool St?).

But while not impossible, I suspect that when you start planning it out properly you'll find a trip like that might not leave you with much time at the museum at all.

There's an offshoot of the IWM in South London, which is good for a short visit - might be an alternative.