500k push/pull audio taper pot for the volume....
500k linear taper pot for the tone....
You're kind of limited with what you can do with only the two knob slots... Is your 3 way a Gibson style 3 way or a Strat style blade switch??? If it's a blade switch like a Strat style guitar you could possibly skip the push/pull pot step entirely and go with a SwitchCraft SuperSwitch and do all your coiltapping through that... So you don't ever have to push or pull on a pot... You'd just have to flip the switch to where you want it.
If I had a 2 knob, 3-way switch, dual humbucking guitar... this is what I would do...
I would go with the SuperSwitch:
http://www.stewmac.com/shop/Electronics,_pickups/Components:_Switches_and_knobs/Super_Switch.htmlWired so the 1st position is the neck coil tap, the 2nd is the whole neck humbucker, the 3rd is both buckers, the 4th is the bridge bucker, and hte fifth is the bridge coil tap.
Make sure you get your humbuckers in a 4 wire configuration rather than the 2 wire...
Another neat trick that I would use to trick out your guitar a little further would be to use concentric pots...
http://www.allparts.com/categories.php?cat_id=616&cat_name=500K%20POTS (Part # EP_4586-000) Since you only have 2 knobs your tonal options are pretty limited within that... Concentric pots basically are two pots that are stacked on one another... If you've ever used an old cassette radio that had big knobs... where the center knob was the volume control and the outside knob was the balance or fade control... that's a concentric pot... You could turn your 2 knob guitar into a 4 knob guitar without drilling into the body. You could wire in individual volume knobs and individual tone knobs... giving you much more tonal diversity.
Another option aside from the 5 way SuperSwitch would be the MegaSwitch
http://www.stewmac.com/shop/Electronics,_pickups/Components:_Switches_and_knobs/2/Megaswitches.htmlOr you can drill a few holes, get two on/off switches and wire individual coil taps so you can have the maximum tonal possibilities there are...
There are tons of stuff to do when it comes to wiring... especially when you get into series and parallel/in phase and out of phase type stuff..
Just some food for thought there though...