New engine or cylinder head M13A

I have had a basic look around for loose belts broken exhausts etc and it definitely seems to be coming from the top right hand side of the main cover. The sound is at engine speed.

You could ask a hundred people and everyone will have different ways of trying to diagnose engine noise etc, apologies if this is unwanted advice. 

I wouldn't fear the worse as my Jimny was sold to me as needing a replacement engine, and I was very nearly able to get it running. I only went for the nuclear option and did an engine swap as I wanted to enjoy driving it quickly and the compression was very low . 

I'd be leaning first, to check one of the ancillary machines isn't making a noise , anything with bearings or a pulley, alternator, power steering pump , aircon etc. 

I'd take the spark plugs out to try and give a clue of what's happening internally. A bit more involved, but you could take the valve cover off and see if the timing chain is tight . There is zero movement on mine. Don't worry if the coloured links aren't in line - That's done to aid fitment, I initially spend ages wondering if my engine was mistimed or the chain had slipped and it hadn't. 

I brought my Jimny on 47,000 miles, described as a non runner and poor compression . One of the spark plugs was coated in what can only be described as black tar and looking though ports the cylinder head was dirty . I priced up the parts for a replacement cylinder head and the work involved, sump requires removing I believe, manifolds etc, retiming it, price of the gaskets, sealant etc and I found it more cost effective to fit a replacement engine. £300 off eBay delivered from a dismantler.

Enjoyed doing the work as well. 

 

I would say drive it till it's terminal 
Lots of M13A engines around 
Or upgrade to M15 or M16 

Reason labour costs to find and fix your problem 
Compared to a relatively easy engine swap 
Unless you can do all the work yourself 

Ok so spark plugs out and cam cover off with no obvious damage to see. Is it safe to turn the engine over with the key with cam cover off and plugs out to see if anything appears ?

I'd put a bar on the crank bolt and rotate it by hand first then it's easier to see anything really obvious.

turned it over on the key and the noise went away. As soon as I put the cover back on again and actually started the engine the noise came back ( probably due to the engine rotating faster ) Next test was to take the alternator water pump belt off. Noise went away. Hurrah. Turning the alternator by hand bearings all feel good so all things are pointing to the water pump having failed or a bit of foreign matter init. Task tomorrow will be to take the rad off and get my hands on the water pump.