My understanding is that there was a two-fold plan at work, here. Get ready for a long explanation:

As Dave mentioned, this period saw important changes to federal and state auto regulations. Among these were the mandating of PCV valves in NY & elsewhere, replacing old-style 'road draft tube' ventilation. But the biggest problem for Ford was CA's new, lower standards for hydrocarbon emissions. Dearborn's 4v engines were already proving somewhat problematic in this regard, so it was no surprise their workhorse 390 needed some tinkering to pass.

And this was further complicated by another change for '66: all grades of US pump gas had been reformulated. Premium fuel, by now considered the de facto touchstone of any 'personal luxury' car, was bumped up from 99.0 octane to 99.8. Again, as with the revised administrative laws, several Ford mills required substantial rework to meet this challenge....or to take advantage of it, as Ford's sales literature said at the time.

So, the base 390 4v received a new carb, heads, intake, cam and valve springs....not to mention the in-line fuel filter & baffled oil pan. All of this was designed around twin engineering ideals of (1) improving warm-up & general driveability while (2) promoting lower emissions, both at idle and at speed. This latter goal proved an elusive one, revealing the stalwart Autolite 4100 as the weak link - hence 1967's intro of the 4300 series and 'IMCO' engineering.

....but that's another story. Hope this helped. :-)

Mr F