Check crankshaft end-play & see where you are, if it's too tight, the bolts can work loose. Changing gasket thickness is really the only simple way to change the end-play to loosen things up a bit. You should be able to grab the crankshaft & feel a slight amount of play when you push & pull against it. If it's tight, then you will never get the bolts to stay in place.
This is what I made to check on the new build, it's crude but works well enough. 10-15 thousandths is about right for the motor to run well & not have problems. It's just a cheap ($16.00) dial indicator & some scrap aluminum that bolts onto the side cover to check the slop.
I went with studs on the new motor (but it's not run yet, so take what I'm saying with a large pinch of salt) & used red loctite to set them in the block so they stay put for good. With the studs & loctite, you can run 20 ft/lb on the flange-nuts for a better grip & not worry about it. If you continue to torque the bolts into the aluminum case, it can wear out the holes over time & create problems. Blue loctite is the best option for bolts & aluminum if everything else is good, but check how tight the crankshaft end-play is first, to make sure there isn't a lot of force pushing out on the side cover which is working the bolts loose.