early 4.6l B-series head question???

I would say yes, you need to keep the plate. The idea of the different runners is to better tune the intake for a wider operating range. This allows the engine to operate on one runner during low speed operation for better low rpm torque and around town manners, and still allows another runner to open up and feed the engine more air the upper rpm range. Often, the runners are a different diameter or length to tune for a certain operating band. Shorter and fatter primaries favor the high revs, while skinnier and longer primaries favor the lower rpm range.

Looks like the B heads have two intake ports for each cylinder cast into the head itself. Sure, you could build a manifold to eliminate the plates and dual runners, but this would likely hurt the low and mid range torque quite a bit.