First of let me say that the SCCA tried to do the best they could with a handful of people where Nascar would have a small army to inspect roughly the same amount of cars............... Did they overlook stuff, yes they certainly did I can remember being at St. Jovite in 69/70 when one of the local track stewards who was helping SCCA with the inspection produced a set of body templates to make sure that all the cars conformed to manufacturers specifications. The local guy was told to remove them from paddock as they had no intention of using them, obviously SCCA did not want to open a big can of worms.
We all know about the acid dipped bodies and creative suspension mods and I am fairly sure that for the most part I think that a lot of teams were using over sized engines....... To the best of my knowledge SCCA never bother to test engine displacement till 1972 after getting a lot of pressure from the independents. I am not sure about Penske doing a car switch but it certainly would not surprise me .........But I do believe they were caught being 250 lbs underweight in a post race inspection at Sebring.
As far Smokey Yunick is concerned from what I read he was quintessential cheater but I don't think he had any influence in the Trans-Am series.