The OEM bottom bracket used a 109mm, symmetrical spindle. That will only reduce the protrusion by 2mm per side, which would typically not be very noticeable. There are very few exceptions to the two degree taper but different companies used to have different end widths and lengths for the taper, which would affect how far the crankset would sit onto the spindle. It sounds like you may have a compatibility issue between the crankset and spindle. What make and era of spindle are you using? If you're using a modern spindle and are planning on using the same brand, then all you need to do is reduce the overall length by twice the distance that you want to move the crankarms inwards on one side.