hey there....
i wouldnt worry about the rear safety tang not sitting flush with the stock... mine doesnt either... its purely cosmetic... and i am pretty sure milling down the action pillars is gonna be far more work then adding something like bedding compound or filler around the safety tang on the stock and then shaping or sanding it to fit up around the safety tang to make it look good... keep in mind that you would have to mill down both the front and rear action pillars at a taper with minimal material removed at the front of the front action pillar gradually removing more to the rear at the right angle to keep the mating surface to the action true just to get the safety tang to sit flush with the stock... so ya if it bugs you that it isnt flush at the rear tang just add some marine tex, acraglass or other sort of bedding compound to the stock around the tang and after it sets grind/shape it so you have a smooth flush fit.... keep in mind that you should have that rear tang free floating from the stock (not contacting the stock) so if you do bed around it you should then remove any of it that is contacting the tang (enough to slide a dollar bill between the tang and the stock. i just left mine alone because i'm lazy and dont care if it looks a little off....
as far as the magazine box goes... i'm still a little confused... you said:
"so it can accept a center feed long action from a staggered feed model"
do you mean this is a straight up factory center feed designed receiver and centerfeed blind box mag? or are you taking a factory stagger feed receiver (old action design from before they came out with the centerfeed design) and you are using a new center feed box mag? or were you referring to the stock when you said: "from a staggered feed model" ..... this is a top load blind mag model right or are you talking about a detatchable magazine?
well anyways i guess it doesn't really matter either way if the mag is causing problems i'd grind away at the mag well not the magazine... the dremmel is your friend!
if i am envisioning your description correctly the magazine doesn't have enough room in the mag well to sit forward enough to properly mate with the receiver so yah just get a good coarse bid and grind enough aluminium out so things fit....
if its more that the mag well isn't deep enough, even better, the bottom of the mag well is all plastic and its pretty thick so grind away at that just enough to get a snug fit and your golden...
once you got things in line and the mag functions right i'd lay a little bedding around the base of it (with release agent on the mag so it wont be permenently fixed in place) so the box will be held exactly in place when the action is torqued in place..
sorry for the long post
orch