Find a bit of this a bit hard to understand. "Thrown a stud". Does this mean the nut on a stud has disappeared, or does it mean the stud has loosened in its hole? The stud can't have gone anywhere as you mention later on about it needing to be removed through the manifold hole.
If you've lost the nut but the stud is still well tight in its hole, I would leave the stud well alone, there is otherwise a chance of stripping the thread in the head or, worse still snapping the stud when you try to extract it.
If the thread on the stud is intact, you only need to replace the nut, with a lock washer and probably a normal flat washer under that. 18lbs/ft torque setting, which is a bit small for a click type torque wrench so you may need an old fashioned indicator type.
If the thread on the stud has gone you have two choices, neither of which is fun. The proper thing to do is to undo all the other nuts and take off the manifold, (there is more to it than that, see Haynes manual or other threads) then extract the stud as best you can. Once the manifold is off you can use the nut-and-locknut method, if you are lucky but you will need to soak the stud where it goes into the head over and over again with WD or your favourite penetrating oil, before attempting this, or you will strip the thread in the head or snap the stud. There are patent stud extractors on the market. I have one, it ain't much use and it bug5ers up any thread that might be there. Remember to turn the stud a tad clockwise to crack the corrosion holding it in before trying to wind it out and be prepared to do a bit of back and forth movements rather than trying to wind it out all in one go. If you are lucky and get it out you can replace it with a new one. If not, you are in the world of drilling out, using "easyouts" etc etc. (SOOO badly named those things.) Lefthand threaded drill bits can be handy, but these drill bits come in really weird sizes and so do easyouts so watch it if you want to use a combination of the two. Once that is done you will have to carefully drill the next size up to retap bigger and then put a bigger bolt or stud in. Then you absolutely will have to drill a bigger hole in the manifold. I had to do this job last summer and it did not go the way it was meant to!
You mention a bolt. There is no bolt, it's a stud and a nut.
"ground back true". Are you referring to getting the manifold ground back true again? if so any machine shop should do it for about £30 cash. I'd also widen the holes in the manifold by 1mm for those on number 2 and 4 cylinders and 2mm on number 1 and 5 cylinders.
If there is no, or little, thread left on the existing stud, there is a slightly less conventional way around it which really is not in the books but may get you temporarily out of a hole if not even for longer, and that is to diecut a thread the next size down onto the stud. Then you can fit a next-size-down nut onto it. With appropriate washers and a second nut to lock the first that might be OK. (Now I am waiting for all the other members to tell me that is not the right way to do it. They will be right but it cannot make it any worse I think.) For penetrating oil I prefer a mixture of ATF and acetone, (nail varnish remover). Brush it on. The acetone is really penetrative and the ATF is thin but highly slippery. Best of luck.