See my previous posting here, it may be of some help..
brake-calipers-t26832.html
(Apologies for using the word "Once" more than err, once in that).
I have a sleeved M/C and found no issues bleeding it after reassembly and with everything in place.
These are the steps I followed on my MK2a (MK3's may be slightly more challenging):
1) Cover all your paintwork with towels, and wrap an old flannel around the master cylinder.
2) Make sure both pistons are as far back as they will go, (this reduces the amount of air in the system to start with, ((and will not block the ports)).
3) Open the bleed nipple max one turn, and attach your bleed tube which has it's other end immersed in clean brake fluid in a jar.
4) Fill up the master cylinder, then just holding the ball end of the lever between thumb and forefinger use very short and fast "pulses" on the lever watch and as air begins to rise out of the intake & bypass ports. Obviously keep topping up the fluid.This stage may take 5 - 15 minutes, but eventually air will stop coming out, and you will start to see spurts coming up through the fluid as the master cylinder is purged, and begin to feel a bit of pressure building up. At this stage you may also see some air bubbling up in the jar
5) Start using longer strokes on the lever in order to move more fluid down the hose (topping up all the time).
6) When you see air bubbling up in the jar, depress the lever all the way, hold, then close the nipple, let the lever out, open the nipple, depress the lever, repeat process until the lever starts to firm up.
7) Once you have as much air from the system as you think you can get, pump the brake lever until it's at it's firmest, hold it there then use a ratchet luggage strap or cable tie to hold it under pressure.
8) Come back in 24 hours to a lovely firm lever.
Hope this helps,
Cheers,
cliffa