I have a similar setup, but with a 28T large freewheel cog and a 30T small front chainring. Even that is stretching the limits of what the derailleurs are capable of. It's not clear to me what exactly the problem you're having is. If the small chainring is 3 mm from the stays, then obviously you can't use a narrower BB spindle. Note that Sheldon's 45 mm chainlink measurement is for a Shimano setup, so is not necessarily correct for your setup. Also, he says "You may need to move the right crank out farther if the inner chainwheel rubs on the right chainstay, or if the chain rubs on the next larger chainwheel in any combination that you use."

It sounds to me that the problem you're having is that the FD can't make the jump from large to small chainrings. This would depend a lot on how big your largest chainring is. My Campy NR FD is barely managing my 52-42-30 setup. If you have a 52-42-28 on there I'm guessing that you're not going to be able to make it work. Better to go with a different FD or perhaps a smaller large chainring.