the 427 was sold as a performance engine and was the major "status engine" for Ford in NASCAR and NHRA), the 428 was (at the time) more of the big car low rpm torque motor with a very mild cam. the Cobra Jet 428 had a bit bigger cam but it didn't come out until later in the 60's (well after the last Shelby Cobra was built). I assume as 427's became scarce Ford offered Shelby the 428s toward the end of the run, Shelby being pragmatic probably rationed that he'd have less liability with the milder engine and they were still more than enough power for the 2500 or so pound cobra.
the Side oiler has priority mains which means the mains get
oil first (directly from the pump) and not from the lifter galley's.
Better for high RPM racing and (most importantly) it eliminates the possibility of losing main
oil pressure in the event of a valvetrain failure
also the 427 from the factory displaces only 425.5 CI and the 428 displaces 426.5 CI.
They called it the 428 to avoid confusion. Maybe they thought if you measure an engine hot verses cold it probably expands another cubic inch , lol