Thats a yes to the drill bits, and a no to the bore gauges
Is it as per the link higher up in the thread? Brain is a bit fuzzy....
I'm not sure, had a glance and didn't see any particular instruction for timing but I didn't look for long.
Take the rubber cover off the timing chest to expose the timing pump sprocket.
You will note 3 bolts and a lozenge shape opening which opens into a round hole. Use this as your timing mark so to speak. The first thing you need to do is look at the hole in the inner part of the sprocket in relation to the driven part of the sprocket. When you insert the drill you need to be aware of which side the drill is tight against or you could get this wrong (not badly though so don't panic). If when you look into the sprocket hole it looks like the outer and inner are basically perfectly in line (factory) then you would want to insert a drill bit that will slide in perfectly straight with more or less no movement in it at all. However if the pump has already been tinkered with it is entirely possible that the hole in the inner section will be partially overlapped by the outer piece. So your drill bit will be hard up against the lip on one side and the edge opposite in the hole on the inner. So this dictates how you chose a drill bit to adjust your timing. If you are dealing with a seriously retarded engine for example, you will be wanting to put a bigger drill bit in than originally you were able to put in as the "Original setting". From what I have told you above you should now be able to work out what you are doing in order to fairly simply but with some form of measurement, tune your engine.
So take the first drill bit and keep it as "Original setting". Now work out what you think you need to do to your engine, it was a week ago I last read through your post but I think you lacked higher speed power, I don't think there is a mention of smoke but lets say you feel the fuel timing may need advanced (does your engine clatter much when you give it the beans?) - then undo the three bolts a little, just enough to stop them clamping the parts of the sprocket together. Now looking at the pump from the front of the engine, in order to advance timing, you want the pump rotation in relation to the rest of the engine to be earlier, so in relation to the driven part of the sprocket you want the inner part of the sprocket to be moved CW slightly, so that means in relation to the rest of the engine the pump is now a little further forward or advanced. Now, what you need to do is slot something into the hole that will let you advance the pump a measured amount, so if you look into the slot and think that the plan here is to rotate the hole in the back section CW a little.
Depending on how your engine is currently timed it may be that "original setting" drill is hard up against the metal on the LHS of the driven part of the sprocket, so that means that when you rotate the inner part of the sprocket the gap will get bigger, so slot in a drill 0.5mm bigger than the "original" and take a socket and ratchet to the nut in the middle and move the pump (you may need to tap the ratchet a little to get it to break free, it could have been bolted up like this for 20 odd years) CW a little until your drill bit will fit in dead straight but tight up against the driven part of the sprocket and the opposite hole on the inner. Now tighten up the 3 bolts and remove the drill.
Take it for a spin. Take it for test drives on a hot engine, this way when listening and feeling for the effects of the diesel timing you are doing so on a hot engine to give you a majority running condition tune. For example a cold diesel will clatter, you could actually through timing remove this clatter noise by retarding the injection timing a fair bit, but when the engine heats up the timing would be so retarded it would sound very quiet, black smoke hard to start and could mis under certain load conditions.
Hope this makes sense. I have done this several times and had excellent results, I think I have broken it down into enough pieces of information that it is clear enough what is being done. Don't be too worried about getting this really badly wrong, you can always revert to a factory tune. Another note, if you suspect your adjusting using the pump nut has loosened it, nip it up with some locktite. I have never had one come undone when rocking it back and forward on the ratchet as it is (should be) done with thread locking compound.
<Edited 13/04/16 for some typos and to make a sentence a little clearer>