The 6mm bolts on the crankcase should be torqued to 6 or 7ft/lbs. You're right the longer threaded end of the HD studs in the case, respect the torque value. Looks like whoever built up those gasket kits had some extra o-rings.
I suggest you visit an online parts fische and figure placement out from there. The two cylinder base o-rings, tach drive, left side oil gallery plug are all similar but not the same size.
You're also correct about gasket thickness, 0.043" & 0.020". Here is what I do to measure piston height in the bore. I used two pieces of 1/4x1.25" steel bar and drilled holes for the front & rear studs and with spacers clamp the cylinders to the cases. Start with a stock gasket, install the cylinder over the pistons even with one ring. Use a dial indicator and attach the magnetic base on the steel bar. Indicate the cyl. deck right at the bore edge and with the pistons at TDC slide the indicator onto the piston. It takes a little practise to do this and get a good reading. The last two 550 engines I checked (with stock pistons) were 0.016" below deck. You can then order different thickness base gasket to adjust piston/deck height. I use the viton coated steel and have 0.010, 0.014, 0.020, plus you can stack them to get close to what you need. Machining the cylinder deck flat first is a must. You can remove more later if necessary.
You'll need to check piston/head, plus piston/valve clearances with a different piston dome too but unless your building crazy compression I'd recommend a CFM head gasket. Copper comes in different thickness which can help with the mentioned clearance issues but will never completely seal. They always weep a bit of oil.
Measuring all the clearances takes time and patience but if you're straying from stock pistons, is a must. You may need that piston down the hole a bit if it is domed.
Have fun, good luck.
