In that spot, and 3 others like it, there shouldn't be a bolt at all, but a stud; 6/58. The stud would be threaded into the head, so the bottom end of the stud may just be visible in that open part of the hole in your picture. The bearing cap goes on and a nut is threaded onto the stud. So the bearing caps are held on by a stud and nut affair on the front (exhaust side) and a bolt only on the back (intake side).
MCRider: In looking at my engine and referring to the parts diagram, I'm fairly sure that the bolt that's sticking down and in the way of the plugs is #90054-300-000 - which is called up as a 6x58 Flange Bolt. Goes through the camshaft holder and down into the cylinder head. I measured the bolts - they're 6x58. Am I missing something?
Did you have a curious oil leak out of the middle fins of the head?
Ah, yes. Actually, I've got oil leaking all over the place. The pucks were quite hard, and will get replaced. PO had replaced all gaskets but hadn't cleaned off previous to his work. So I have a feeling that shoddy workmanship has led to much oil getting displaced down the front of my engine, down the back of my engine, and all along the downtubes of my frame.
I'm guessing that you are looking at the page for the "camshaft and holder"? Bolt #4 is indeed the bolt you need and its 6x58. Those bolts hold down the cambearing cap and they go in the intake side. On the Motogrid fish, the quantity is not listed as they are no longer available, but if it was it would say (4). If you'll notice paired with each bolt is the 6mm nut that goes on the exhaust side. The stud that they (4) go on is not on this page.
You have to go to the "cylinder head" page of the parts book. It is #13, a 6x58 stud part number 9005
5-300-000. Do you see it? They are no longer available either. A real curve ball. So the bolts only go in the intake side. The stud and nut affair goes in the exhaust side. If you are having mysterious oil leaks for sure suspect the pucks. But also, once the seal of the factory stud-in-head is broken, you have the very real (I know) chance of oil wicking down the threads of a bolt in the exhaust side, dripping into the fins at the bottom of the hole in your picture, in the plug cavity and exiting the fins at midpoint. At a stop the oil will drip and drain forward as the engine is tilted, at speed it will blow out and back all over creation.
My suggestion is to try and get those OEM studs again, clean the holes mercilessly, with a QTip and acetone or whatever, and reinstall the studs using a locktite type thread sealer. Tighten them into the head only far enough that you have enough sticking out to put the nut w/flat washer on top of the bearing cap. You may need to dry fit them to be sure of install depth. Let the sealer dry hard before putting the nut on and torquing it.
Don't worry, it will still leak.