Since you've already had it all apart, ask yourself how careful you were about cleanliness prior to and during reassembly. If you feel that you were quite cautious, you can probably skip disassembling your machine again.
.003" is not much, especially over the width of the table. Most parts that a person makes with a mill this size are small enough that you would not even see half of that across the width of the part, and most parts have tolerances of more than .003" to begin with. So ask yourself if you seriously cannot live with that .003". There is also a big difference between NEED to be rid of that .003" and WANT to be rid of that .003". Myself, I know that my parts typically have greater tolerances than that to begin with, so instead of spending my time trying to dial in an older machine, I'll spend my time making the things that I bought the machine for in the first place.
If you really want to dial it in, you could try adding a shim between the head and the ram, but keep in mind that a very thin shim will make a huge difference at the end of the spindle. It is probable that a .001" shim will over correct your problem and will tilt the head even further, but in the opposite direction. One of the other posters mentioned making a spacer disc that is slightly wedge shaped to go between the head and ram. This disc would need to be very carefully made, ground completely true on one side and with a perfect wedge shape of maybe .005" or .010" difference on the other. This may not be the best explanation, but I don't know right off of any other way to say it.
