I went through a hard time after re-sleeving my OEM master cylinder on my 850. After many days of fiddling/re-bleeding etc., turned out to mainly be due to the master cylinder primary seal already being past the smaller/towards bike centerline hole when the brake lever was at rest. Had to file some material off the lever where it made contact with the piston. Ideally, you want the primary seal sitting just a mm or two away from the smaller/towards centerline hole so that as soon as you begin applying lever movement, the seal passes that hole and therefore seals the oil in the brake line to the caliper.
Presumably, if you bought a professionally modified cylinder, this should have already me setup right...however, if you are using a lever with a different dimension in the critical areas, then all bets are off. You need to take some careful measurements with a caliper to assess where the seals are with respect to the two holes with lever at rest.
If you find everything looks correct, then the most likely situation is you still have trapped air....took my several more days to finally get it all out....try flicking the lever rapidly for 5-10 minutes with left, then right full steering lock (to change the caliper angle to help bubbles find there way out). When I did this, watching the two ports in the reservoir, I saw a few tiny bubbles escape...even after bleeding multiple limes bottom to top using large syringe. Another tip is to keep brake lever pulled in using elastic band with steering held at full left lock overnight...again helps trapped micro bubbles find their way up and out.