APN Exhaust manifold
 

I am new to the XJ family, and this isn't the reason i'd like to have my first post but just got mine back in february but she needed work. started off with new muffler and cat, injectors, TPS, valve cover gasket, sway bar links and rear leaf springs. that all went easy and was pretty fun.
The second thing i bought was a APN exhaust manifold, I read all over and on my 98 the only issue i expected was the bolt to the right of the center tube being a pain. I was prepared and got it on with a ratcheting wrench pretty easy.
This is where my issue came up, after putting her back together when I turn it on I rev up to 2-2.5k, then it drops down to 750-1k but idles rough until warmed up.
I assumed i didn't have everything lined up right so i bought a new FelPro gasket and redid the whole thing, issue is still there. so i did it again for kicks and giggles. At this point i couldn't miss work so i had to put her back together, my mechanic says it sounds like a vacuum leak, i have checked all lines i can find as best as i can. It seems the leak is coming from the manifold, a buddy looked at it and noticed right away that the new manifold is thicker than the intake (2-3mm) and the washers are not sitting flush.
So as far as i can tell that is the issue, but can not find anyone else who seems to have this issue. Have any of you had a issue like this or have any ideas?

might be the intake isn't properly seated, check clearance between the intake and exhaust manifold. The idle issue is pretty typical of a poor seal on the intake. usually it's more of a problem with the 99+ intakes but not unheard of with the earlier intakes as well.

The clearance is definitely off, thats what i meant by 2-3mm difference. The exhaust manifold is thicker than the intake all around, I don't really have the means to grind it all down.
I seem to only read good things about these manifolds which is why I bought it and can not find anyone else with this issue, which is why I am so confused.

Did you use the stock cone washers? They will allow for the flange thickness differences better than just a normal thick exhaust washer will.

Yes I used the stock cone washers.