Ive started to get vibrations when braking, so I took the wheel off and got into the pads and I noticed there was a big score on the inside pad (see pic) the outside pad was fine The disc seems fine so don't know what caused the big score on pad, any ideas? 

The bit that has worn down on the pad looks like it was caused by a rusty part of the disc . I note your pic does not show the disc face that that pad runs on

I ran my fingers through both sides of disc and it was completely smooth- just throwing this in here but I bought a single nut off eBay couple of years ago cause the original nut was about to strip- eBay nut was fine but was higher than original nuts(see pic) and today when I was putting wheel back on I tightened four nuts to around 120 newtons but the eBay nut wouldn't tighten it wouldn't click at 120 I thought it would just continue to be tightened until it broke? Has this ebay nut caused the scrape on the pad? Thanks

As above, the back of the disc will probably be ruined on the very inner edge   Have a look with a mirror if you can't get your head in there.

The nut sounds cross threaded.  Basically it'll 'jump' over the threads at a certain point instead of tightening any further.  At least, you want to hope it's the nut...if the stud has gone that's more difficult to change.  Anyway, this means the wheel and brake disc will be slightly out of balance in one quarter which could cause your wobble.

Thanks for replays do you know the best place to go to get pads and discs?

If you want to collect them asap, Euro Car Parts or GSF are probably the easiest places, and I'd stick with Pagid branded myself. 

If you can wait for delivery, there are loads of places online worth checking.  Always worth shopping around for the best price.

Thanks

If using Euro Car Parts don't forget to put their discount code in the space in the basket.  Code will be at top of the page on their website. Prices without code are expensive compared to others. With discount code it's a normal price. 

👍

I got these when I had my mk2 couldn't fault them. 

https://www.ebay.co.uk/itm/232381192830