If you didn't bench bleed the master, then you've got a bit of a problem. It's very difficult to bleed one properly with it connected to the system. Not to mention the fact that you've now likely pumped the lines full of air. And yes, the best way to cure a residual pressure valve problem is to rebuild the master again with a fresh, new kit. Start with that, repair any leaks in the system, and rebleed the whole system from scratch. When you're bleeding, make SURE that you don't run the master dry or else you'll have to bench bleed the master all over again. About three good pumps is about all you can safely get before it'll need topped off. I know the brake hydraulics are a pain. I just bled mine the day before yesterday after working on the system on and off for 18 months. A little air anywhere in the system will cause pressure problems. It just takes patience! Here's a link to the proper bleeding sequence:
http://chevy.oldcarmanualproject.com/gmc/5559mm/5559mm172.html