Hughes Converter Issue

Bob may be correct. Contact Hughes and see what they say, and the reason (should be) the mounting is different, is the 3500 stall is probably a 10" converter, where the lower stall may have been either a 12" converter(with a narrow ring gear) or a 11" converter with the wider ring gear. I hope when you ordered the 3500 stall converter, you gave the supplier ALL INFORMATION your engine-rear axle ration and tire size. Any mis-information will not get the converter you need.
Over the years I spent in the industry, I saw many so called bad converters because the buyer didn't give the converter builder the right information. Another quick question, did you buy the converter new, or used/