Studs are great for several reasons
#1, they preserve the threads in the block. When you are using the bolt, there is a whole lot of friction in the threads...you're building friction and tension at the same time. You are also torquing against a coarse thread (7/16-14). With the studs, you're block threads are never exposed to friction, just tension, so they will not wear. The business end of the ARP studs use fine threads (7/16-20 I believe...maybe 24) so you are creating more tension for a given torque value due to the decreased ramp angle of the threads. 80lb/lbs on a 7/16-20 thread will yeild considerably higher tension on the faster than 80ft/lbs on 7/16-14 thread...not to mention the surface finish on the ARP stuff is considerably nicer than any threads in the block, so you have less friction. Additionally, ARP wants you to use their moly lube on the washer and threads, which further decreases friction. I'm pretty confident that 80ft/lbs on an ARP head stud nut will most likely result in more than double the tension that you would get with 80ft/lbs on a factory head bolt. Much of that torque with bolts is aborbed by bolt twist and frictional losses in the threads and under the bolt head. More tension holding stuff together means a more ridgid assembly.
The problem with studs is that since they allow more tension, they will cause the block to move differently after things are torqued....which is why it's important to use the same type of fasteners on your torque plates and mains when machining the block that you use when assembling the block. I've seen multiple times where the use of studs in the mains caused the caps to twist due to the higher clamping forces generated...and the block then requires align honing or boring, which introduces it's own set of problems. If you can get lucky and find a block that still has straight round mains with studs in 'em before any main work...keep and and savor it for ever. If you do any cylinder machining, make damn sure that the main studs are torqued using the same lube you plan on using and to the same torque spec you plan on using. Main studs pull the cylinders in all kinds of funny shapes, and you want them round after it's assembled.
As far as sealer goes, I use Toyota FIPG (toyota version of silicone)...I used to work for toyota and this stuff is so far ahead of anything that permatex can bring to the table it's amazing...you can make a tire out of it I bet. It's about $25 a tube though...but toyota glues engines together with this stuff instead of gaskets and they don't leak after 200K miles...so it's good enough for my head studs.
I always chase all the block holes, then clean with brake cleaner and dry with compressed air. Make sure the packing oil is cleaned from the threads on the studs, apply some silicone and thread in the stud. Even regular ultra black seems to work fine. Don't use that teflon thread sealer though...it doesn't work for shit....cost me a motor once because a stud started seeping water under a valve cover.