I ran into a similar clearance issue with my new steel flywheel and aftermarket clutch. I was reluctant on grinding down flywheel bolts, so contacted ARP and bought bolts that have a reduced head height. Also removed the flathead flywheel locating dowel retainer that gained over .050". Just lightly stake the flywheel dowel holes to prevent any movement. Overall gain was over .100" that resulted in the extra spring clearance I needed.
I never run the lock wires, I just torque em up with loctite. Never yet had a flywheel come loose.
I got some low height ARP flywheel bolts witch look good they have a nice wide head witch is lower.
How meany lbs should I tighten them to? I am going to use some locktite and leave that steel plate out