You are correct, its the chassis milling, and the front bulkhead that are the defining differences between the 4.0 and the 5.0, also the waterfall and battery holder are different.

All of the important bits that he would be most likely to break, like suspension arms and spindles, are either the same, or 100% compatible. Front spindles, the rear gear box components and the front and rear shock towers are all the same.

For tunability it might be worth getting the 5.0 C and D block and a set of pills. As well as the VLA rear spindles and updated stub axles. Then beat it until the Happy Hole shows up in the rear of the chassis, and upgrade.