Can anybody tell me what bolts here please (3EN2)

That's where the tank cover bolts to the tank below. Look on the (black) fuel tank and you'll see a captive nut. It gets covered by the saddle.

Thanks. Also, are the two rectangular grommets for side panel location still available. If not, is there anything else that can be used??

The original grommets are 90480-01401 and fit quite a few models even if somewhat expensive.
http://www.ebay.co.uk/itm/Yamaha-RD125L ... 1241369940

I am sure I have used these on a refurb though;
http://www.ebay.co.uk/itm/YAMAHA-FZ600- ... 51c8c43eb0

There is a parts fiche here;
http://www.400greybike.com/docs.htm

Sorry, I worded the question wrong. I meant the two rectangular grommets on the sides of the tank cover that locate the front of the side panels. P/N 90480-01514. Is there anything that can be used if they are unavailable.
Cheers

You can try so panel trim or just a round grommet of the right size.
The side panels have a hook at the front that fits into the hole