Engine accessory hardware - from Bolts to Studs/Nuts

I'm finishing up an engine rebuild on a 96 Neon I own. I'm feeling bad about putting old, rusty hardware on a new engine.

I've been considering converting from bolts on the visual areas (valve cover, coil pack, throttle body, thermostat housing, etc) to studs/chrome acorn nuts. I'm not too up on the JDM, yo flat washer look.

I have a bolt replacement guide printed out and am selecting stud length. Would it be safe to go +5mm on the length and hope for the best? Is there a rule of thumb for such a thing that I've never been taught?

Since this a question--and a very good one--I'll move it to the main forum. You should get some answers there.