Well done mate in doing your exhaust manifold.
If your determind to get the broken stud out of the block and DO IT in situ, then you can always use the manifold as a guide !
As you aew well aware, to drill a broken stud out you NEED to be smack on centre of the stud when you drill i to it !
Having a little sleeve made up ( do you know anyone with a lathe ) that slips in to the hole in the exhaust manifold with a 3 or 4 mm hole down the centre of this sleeve will allow you to guide a drill smack on centre in to the broken stud ! Depth can be measured NOT GUESSED, by obtaining a new stud ( which you need anyhow) and just measuring the depth of thread !
As far as being careful of torque setting or values on lubricated bolts, you have to use your common sence here ! A small amount of lubrication will not SIGNIFFICANTLY affect torque value, as these are affected anyhow do to dis=similar metals being used , such as steel bolt in to alloy or cast iron !
Lubricating bolts etc , with a smear of copper grease has many more pro's than con's , due to the fact that dis=assembly at a later date is made so much easier due to the fact that the copper grease slows down , very much, slows down Galvanic reaction between dis=similar metals !
Also bear in mind that replacing your studs and bolts with stainless replacements is even worse than lubricating steel bolts etc !
Stainless has a LOWER tensile strength, and has significantly more drag / friction than steel, so torque values are useless !
Also dont be fooled in to thinking stainless fixings dont rust or react with other metals !
EVERY metal will react ( galvanic reaction) when screwed/ fixed or partnered with another metal, although some pairings will be A LOT slower than others to show reaction !