Bill on my 68 I took the secondary butterfly plates out of the shaft but left everything else intact. For the most part things have worked great. Leaking floats and vacuum leak at the crossover pipe gaskets have been my causes of rough idle. The leaking crossover pipe gasket was the hardest to find since I initially did not think of that spot on top of the exhaust manifold as an area for a vacuum leak. You might spray carb cleaner around every spot that has access to the intake manifold. I also have had #4 plug from the front carbon foul from time to time causing idle problems. You might check the coil too. On one of my 70's Chevys the coil was causing misfire problems especially on hot days. I also have the Pertronix but it has never given me any troubles.
David Barnes
68 E-Type FHC