John,
This is a problem many newcomers to the Myford 4-way have found.
The 4-way was originally designed to use 5/16" tooling, of the "old-fashioned" type, as you have found anything more won't go down to centre height. The slot will of course accept thicker than 5/16".
My 4-way has the inner bottom edge of one of the slots milled away by 3/32" to lower the height of thicker tooling. As the 4-way is bolted down tight on the topslide I don't think this weakens it.
Phil