WD40

Not a fan of using spade connectors on motorbikes. They always seem to corrode or break after a few years.

Are the battery connections tight?

Nothing obviously wrong so far. Oil is getting up to the top of the engine. No signs of cam lobes hitting anything. Cam chain tension seems fine. If it was too slack you'd see the chain riding up on the exhaust sprocket as you rotated the engine. It seemed to stay tight to the sprocket as you rotated the engine so it looks ok to me. You could flex the chain up and down with your finger. It should be very tight across the top of the engine and down the front. You could start it with the cover off and see if the noise is more obvious. You would have to be careful nothing fell into the engine and starting it would cause oil to spray out everywhere but it might highlight the noise. Another thing you could do that would be less messy is measure the valve clearance and see if any valve clearance is obviously different compared to the others. That could indicate a damaged valve. After doing those two things I think it's cams out and head off and have a look. At that point you have to decide if you want to do it or would it be better bringing it to a mechanic and let them listen to it. All you've done so far is taken the cover off. You could just put the cover back on and bring it to a mechanic and get there opinion.

Glad you got it back! If it hasn't got an immobiliser it is as simple as twist a few wires together and away you go...but don't tell anyone

Have you got a copy of the factory manual? https://archive.org/details/printermanual-yamaha-fazer-fzs600-service-manual-1998 Page 4-6 shows taking the cam cover off. A few bolts and you could lift that up and see if there's anything obviously wrong with the cams/cam chain/lack of oil.

They look cut to me, or pinched.

Hands up anyone that has one of those boxes of assorted o-rings....but it never has the right o-ring in it

So the question is basically can a fuel injected bike stall or over heat if there's a problem?

Worst case scenario if you have to replace the head. I think you'd get a used head and a new OEM head gasket for around £200. It's a pain that this happened but it's not the end of the world you should sort it fairly cheap.

What do think the problem is?

Why does metal hit metal though? Lack of oil. As an example, pistons rings against cylinders, big end bearings against crankshaft, camshaft against camshaft bearings. They all need a thin layer of oil between them or it's metal on metal and they're ruined. I'm just trying to think of logical reasons why, before he did this work he had no noise. Then he drops the oil, drills a stud out too far and straight after he has serious noise. All he touched was oil and exhaust so logically the problem is from one of those areas.

Like the other said take the cam cover off and check if oil is getting up to the cams and around the valves. The cam cover gasket is rubber so you won't need a new gasket

More speculating. You did the oil change didn't you? Are you sure you put enough oil back in?

Yeah you're right they are regular bucket and shim valves not hydraulic ones. The camshaft sprocket is on the middle of the camshaft and down the centre of the engine.

Yeah that's the top of the engine looking down. The bottom of the picture is the front of the engine where the exhaust cam is. The top of the picture is the back of the engine where the intake cam is. The oil feed for the top end is a metal pipe bolted to the front of the engine. The arrow points to where the metal pipe is bolted. Oil from the bottom end goes up through the metal pipe into the top of the engine. It then goes through a passage to both camshafts. The red line shows this passage. The oil comes up where the red dots are. The camshafts have holes in them and are hollow so the oil fills the camshafts. It comes out holes in the camshaft to lube all the journals. You can see the holes in the camshafts in this picture https://i.ebayimg.com/images/g/XbwAAOSw-jFaDYdG/s-l1600.jpg The oil then leaks out from around the journals to the area around the valve buckets. This lubes the area around the buckets. It then flows back down to the bottom of the engine. The blue arrows. If oil was leaking out of where you drilled instead of staying around the journal and around the valve buckets you could be losing oil pressure around the exhaust cam and losing the oil that should be around the valve buckets causing the top end noise you're hearing. It's just a theory, it could be wrong.