http://privateerpressforums.com/showthr ... ties-Mk-II
This link fully explains the rules and sequence for the deathjack. It supports the rulings with official quotes, though they are mixed in with a mishmosh of posts arguing about the topic.
1: Souls transfer into focus(this can take you to over 3 focus)
2: Allocate focus from Warcaster(check focus quantity both before and after allocation)**if it has 3+ focus before this step you cannot allocate focus to it during this step
3: Generate focus from skulls in arms (this can take you over 3 focus)
***All focus is stored on the cortex even if generated by arm skulls, destroyed cortex cannot be allocated focus but can have it replenished or added by claws even if its unusable
Thus your mainly gaining 1-3 free focus(allocating the difference) +2 from skulls. Should you manage to harvest 4+ souls in 1 turn without using them to heal damage with DJ's ability, you would then on the following turn be unable to allocate from your warcaster however you would have more focus than the typical 3(+2) limit
Also of note, official ruling is if Deathjack makes a trample it only gets souls from models within 2" at the final resting point at the end of the trample.