I want to use as many threads as i can so I dont stip the aluminum heads. I have BBk headers which have a thick 3/8" flange. I want to use a 1.25" header bolts so I can use as strentgh as possible. Will these work or will they hit the end of the bolt holes?

 

On mine I could not see anything longer than 3/4" after going thru the header flange without bottoming out, I'd think you could use anything longer than 1", maybe an 1 1/8" total... Just screw one of your original manifold bolts in without the spacer on it and see how far it will go in. With the spacer on them, each bolt should be 1" without going thru the manifold yet.