That's not correct and I would not accept that "they have been building engine for XX amount of years and who are you to questions my experience" Bull crap.

#1 who cares what the installed height is ,if the valve length is wrong it will not work

#2 The intake is to long period .

#3 If they piled up the valve job so bad that the valve is .100 deep in the seat , they have no business selling heads. ( not to mention that you will have brutally bad air flow.

The B1 head is still a in line valve cylinder head. The intake and exhaust rocker arm have the same fulcrum point and are parallel in relationship with the valve .

You should have a 5.400" intake and a 5.400" exhaust .

Get on the horn and make them get you new valves.

The Koffels are pretty good at fixing there mistakes ,you just have to call them on it. ( If that was the vender that sold you the parts. )