Hi again John,

Without a doubt i'd say the inline fuel filter could be the issue. I had one fitted for a while also and teh bike was dramatically under fuelling because of restricted flow due to the filter.

If you look at the diameter of the pipe its actually huge in comparison to something with a fuel pump and as its gravity fed must be a crucial link in the chain.
I removed my filter and used a piece of brass linkage to join the pipe but it still played up so i replaced with a similar diameter ployurethane pipe and havent looked back.
Do you find that one cylinder stops firing at all? Also does the engine seem to bog down when you shut the throttle and return to tickover? Those were both symptoms I had.

Regards