So, TTi says my Hookers are made wrong, are they full of crap?

I'm sure TTi never stated that "Hookers are made wrong"!
They probably told you, that the Hooker headers you have are made differently than the headers they bought years ago to use as their mock-up guide. It should have been no surprise that modification may be required. Enclosed in all the TTi header adapter kit boxes is this note…

HEADER ADAPTERS: Adapters to mate Hooker, Hedman or Thorley headers with TTI exhaust systems were designed at Tube Technologies Inc. utilizing new unmodified Hooker, Hedman and Thorley headers. Precision tooling-fixtures were designed to insure exact replication of each different adapter. Should your adapter not fit your header properly, it will be necessary to modify the adapter to fit your particular header variation.

It is known that the Hooker collector flanges have been clocked differently depending on where their headers have been manufactured; US or Mexico.

It would be impossible for anyone to keep up with all the header variations, brands and the different models.