Hi ziggy,

Also, look at 1.2 Limitations. Item (1) states in essence that the code was not intended for use for steels with a minimum specified yield strength greater than 100 ksi.
Welding may not be an option, particularly if high strength, heat treated bolts and nuts are used, and the bolts are subjected to tensile loads.
I don't know the extent of your situation, but the length of the bolts should be such that the end of the bolt should be at least flush with the outside face of the nut when properly installed. Although this statement is in the Specification for A325 and A490 bolts, the same criteria should apply to nuts on anchor bolts.
One way to extend anchor bolt lengths without welding is to provide threaded couplers. Another way is to consider limited carbon arc gouging (air arc) of the base plate surface under the nut to provide full thread engagement.
Of course, as you know, either way must be approved by the EOR, and consideration for anchor bolt resistance to uplift must be addressed.

Another thought along the lines of what Scott has stated in regards to thread engagement... We had to make some special coupling nuts to act as anchor nuts one time when the concrete sub set the anchor rods at an incorrect elevation and ended up with not enough stick through. We had to take the regular coupling nuts and machine (turned them on my father-in-law's lathe) about half of the length of the nut down to fit inside the oversize hole in the baseplate to allow for full thread engagement with a washer. We still had to seek approval from the EOR, but he gave his blessing. Just thought I would mention this as another option as it would save welding on those HS bolts.
John Wright