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Spent most of the day reinstalling heads, intake, etc. I am installing for the first time, OBX headers on my L98. Passenger side went up and bolts went in without issue. The driver side seems to be a problem.
Without physically verifying, I'm led to believe that the bolt holes in the flange aren't 100% correct. I can get a few bolts in, then when I try to add more they want to go in at an angle or not at all. I've tried multiple ways and and I still can't get any more than three bolts in.
Went with the Pacesetter shorties on my 96 LT1 and didn't have any problems like that, althought I can say from experience that while the Pacesetter shorties might look identical, there is a Left, and a Right side. LoL
You might end up having to enlarge the holes a tad where you can't get the bolts in. I have heard a lot of people talk about issues like yours when switching to headers.
If I had an acquaintance or a relationship with an automotive machine shop I might fit the header to a head on the bench first. There's no need to struggle with the "on the car" difficulties if you know someone. Even if you don't it might be worth a call just to see if they might accommodate you.
I noticed you mentioned you were installing heads etc SO I'd guess if your heads were done locally you should be all set!