There is nothing in the way of the stock linkage vs the aftermarket under the floor booster/master. My truck is living proof, I did the conversion 15 years ago. 350 V-8, 3 speed OD trans, daily driver. I just did another one about 6 months ago on a 55. No problem what so ever with bleeding or any performance.
They more than likely provided mis-matched or defective parts!
Fred