Hi Nick,
Brake bleeding can be a right pain when it 'aint going to plan especially when you eventualy get fluid through and the lever has about as much resistance as a marshmallow....
All i can suggest is that you follow any motorcycle brake bleeding procedures, check all the components for any blockages/kinks (including the new lines) and look for any damage to seals etc - my original 1S master cylinder felt ok but one look at the outer seals told me that it had'nt been touched in nearly 2 decades - 17 year old brakes on a 130+ mph bike 'aint confidence inspiring.
Take a look on evilbay and track yourself down a newish mastercylinder if the old one is shot - got a VTR SP1 master cylinder on mine (even uses the same mounting clamp as the original 1S) .
Just one more thing, a local 'Old school' bike mechanic told me that cracking off (then tightening) the mastercylinder bolt as you bleed the brakes normaly can help in most cases.