Capaccio got the jump on everyone again.
The complexity (and potential for conflict and confusion) is amazing.
Eventually, everything that is on the line right now, and everything that goes on contract before 3F passes DT, is likely to need some kind of mod. But you can't afford to wait until 3F is fully developed to start doing that because (1) the services want to start training and getting squadrons on line and (2) by the time you'd finished the new aircraft will be coming off the line in 4.1 anyway.
So what you have to accept is that many, perhaps most, of the jets that go on contract before 2018 will need more than one mod visit to get to whatever the 3F standard ends up being.
But wait, there's more! Before you even start that process, the USAF wants a number of Block 3i IOC jets (a wing?) that presumably have some kind of priority.
How do the depots handle this (at the same time as they start seeing aircraft cycling through for PDM, and learn to handle this new aircraft)? They don't. You'll need to do a lot of mods in the field with contractor/government teams.
If this all starts to remind you of 1950s horror stories of lines of F-86Ds sitting on ramps waiting for radars and FCS, you're plainly an old f**t and an oldthinker who unbellyfeels 5GenTM.