Thanks for the replies guys, gives me a few things to have a look at!

I was thinking of replacing the coil, HT lead and plug cap anyway as the standard ones look very poor quality for a bike that is designed to be used off road and in bad weather. Can anyone recommend suitable replacements that will be a bit more durable?

I have the correct map for my filter set up, but not my pipes. This problem started before I made any mods to the bike but seems to have increased after the filters were fitted. I will probably strip the fuel system too and check for any problems.

Thanks again guys, I will update as soon as I've had time to strip the bike down and have a good look!