Well I have now done some investigating into getting my sills done locally and I have finally decided on a company. I asked for both sides to be done and as I have a red Mk 2 MX-5, year 2000 which appears to have the common fault in red cars of this year, the paint is breaking up and white spots appearing. I also then asked for a full respray for the car. The quotes I have had have varied from £450 cash to £2550 all in. I would advise anyone who has this rust problem to try and get it repaired as soon as possible, if you leave it too long you will then probably have to replace the front and rear panels, which involves alot of welding and possibly exposing other metal surfaces to rust quicker.
The company I decided on was a company in Basingstoke, who deal with Top Spec cars. The quote was for £150 each side for repair and prime and then £800 pounds for a full strip and respray of whole car. I looked at their work on the Ferraris and Porshes they had in their repair shop and they looked impressive. So I thought £1100 all in was not a bad deal. (We will have to wait and see when finished).
I hope this helps anyone who may be out there who may have the same problem as me. There are cheaper quotes out there but you have to decided whether you are going to keep the car for a while( Thats Us) or whether you intend to sell it soon after, which will mean you dont have to have such a good job done.
Hope it helps. If you have any further questions on this subject, email me and I will try to help.