Take a look at the nut also and check that the "bearing surface" that the strings pass across is in a straight line (viewed from the side) for all strings as they leave the nut. Wound strings, in particular, can eat into the grooves and change the intonation. Check also that the action at the nut is not too high. If it is, fretting the lower strings will cause them to go sharper than fretting the higher ones. Frank Ford's site mentioned above has nice pictures illustrating this.
The actions you have carried out tend to suggest that some adjustment is still needed at the bridge/saddle end to improve the intonation. Basically the bearing surface the strings pass over needs to be a tad nearer the end of the guitar and I would take heed of Richard's advice above as he knows the model.