My brother rode and worked at a Honda shop when these bikes were new. The way I remember it, Honda had a problem with guys that didn't bother to learn how to ride bought a new 750 and promptly wrecked it. The insurance companies were complaining to congress to do something about these dangerous machines. The fast fours got a reputation much like the GSXR's did later.
That, as well as exhaust emissions had to do with the tuning changes, Honda in some cases allowed the tolerances like compression and cam timing to slip, some things like rougher ports helped production, some helped emissions, but the result was lowered performance.
When Kawasaki was stealing the sales, Honda did restore some horsepower. My opinion is it was too little, too late and there should have been a SOHC CB900. My brother went on to work at the Kawasaki shop and for a couple years the 900 LTD was king around here.