I would go with 4.88 tires, as changing from 4.10 to 4.56 isn't enough of a difference to justify the cost and labor.
To run the TJ d44, simply cut off all the brackets and buy a pair of spring perches and shock mounts. Install the axle with new ubolts, bolting it loosely in place. Set pinion angle and tack-weld the spring perches. Remove axle and complete the welds.