Yeah, sure sounds like that shop was B.S.'ing you /didn't want to do the work... or they assumed you didn't know nothing about engine and were taking you to the cleaners....New valves wouldn't seat properly in the head? That's what Permatex lapping compound is for and a suction tool or a valve grinder.
Find genuine OEM replacement parts and diagrams for the Air Intake/Filtration 10-27-39 for the Kohler CV15-41562 - Kohler Command PRO Engine, Made for John Deere, 15hp, 11.2kW
www.partstree.com
$30 for 2 lifters and 12 for a head gasket.