Were there studs in it already when you got it or are you adding them during a rebuild?
Regardless, I've definitely run into this issue with a HV pump where I cracked a brand new oil pump housing. I didn't realize the one stud under the pump housing was too tall and it cocked the housing ever so slightly like you describe. Not really thinking it through, I went to tighten it down it cracked right in half. It was only a thread or two to long but that was all it took. yes, it was bottomed out. It's not the washer, it's the stud height. Like said above, I ended up using the stock bolt, nothing else I could do. Maybe some blocks have deeper cap bolt holes? I doubt it!
Hughes even offers an ARP stud kit for the application but amazingly the stud is still too tall (at least in my application).