Blacksheep,
The B707 and the E-3D are quite different beasts, especially when it comes to complexity. The basic E-3D airframe would probably still achieve high-90s reliability rates but it is all the add-ons that hurt. When the B707 was in full airline service there were no restriction or difficulties with things like the toxic insulation on Kapton wiring, multiple aerial fixings, the small matter of a rather large radome, klystrons, IFF interrogators, data links, EW kit, refuelling systems, etc.. Supply chains were full, whereas now most 707 spares are need specialist procurement from diminishing manufacturing sources. The biggest issue will be airworthiness, as policy, practices and attitudes have changed markedly since the 2006 Nimrod accident, and the Design Authority is no longer Boeing for the RAF fleet.
A like-for-like comparison doesn't work.