Torque it up and see what you get
Yep that is all you can do. Torque to the min and see what you got. If a little tighter will get the hole castellated nut aligned just torque it up. The other way is to torque to max end and back off. Lets say you just are too far off? You did one the above and its just not working out.
If the alignment is way off you can "adjust" the washer thickness. There are three ways to do this.
1) Washers have different tolerances, even for the same washer type. Use a calliper and pick a thicker or thinner one as needed.
2) Some guys take the washer and pound it flat to reduce its thickness. It works apparently and one whack of the old hammer does the trick.
3) Another way to go is some guys will sand some material off the washer (flat surface, mirror with 400 grit, wet/dry). That works, but you take off the CAD plate finish on the steel washers. You can always prime it well of you choose this route. DON'T whittle on the bolt or nut EVER!.
So how much thicker or thinner do you need to make the washer?
I think there is 24 threads per inch so 1/24= 0.041. So for every full turn is 0.041. Since the castellated nut has six tangs, you may want change it 1/12th of a turn (half way between tangs). So 1/12th of 0.041 or .0035. So you don't need a big change in washer thickness.
Note: they make thin shim washers, which Van supplies with the bolt "kit":
http://www.vansaircraft.com/cgi-bin...-336-39&browse=engines&product=engine-boltkit
I WOULD avoid going crazy with torquing and un-torquing over and over to get it perfect. Once or twice is OK, but each time you torque it up, you take some plate material off and distort the threads, which itself will change torque and alignment. Also when you handle bolts you can get them contaminated with oils which changes the torque. If you are close be happy.
I never had a problem getting the cotter pin aligned, but I have heard of massive problems? Good luck and don't go crazy with it. I don't want to say the bolts holding your engine on are not important or the torque is not important, but you have plenty of "margin". As long as they are torqued in the ball-park than you are good to go. Sometimes you do end up with a stack-up that's just not ideal and warrants a little adjustment, emphasis on little. Have fun.
George
PS the above is for Dynafocal. Conical is differnt. For the bolts that attaches the engine mount to firewall you can take some material off the engine mount.