Well the other day I took my bike for a spin, and for a bit of carriageway I decided to do the o'l 100mph holding her about 8krpm. After about 5 minutes the bike just suddenly stutters and only runs on one cylinder. So I drop a gear and gas on, still stuttering, then when I slow down, fires back on two cylinders.

Very odd. Ran fine after that.  But she has been backfiring recently every time I've started her up, this is a very recent thing and I'm not sure what's caused it.

Any ideas?

Sounds like it is leaning out. You may have a clogged jet. Sounds like a little maintenance is in order. Get your carbs cleaned or do it yourself. This may help you

http://wiki.gstwins.com/index.php?n=Maintenance.RebuildCarbs?action=edit

Also check your plugs out. What colour are they?

Might be a fuel delivery problem, do you have any kind of inline filter added?

Ooooh yeah hadnt thought of the inline filter. Yes extra tubing and a filter added lol. It did cause problems a while back! Maybe it just couldnt supply the carb fast enough over a long period of time? cheers. 

If it's an automotive filter, remove it, they require pressure from a pump and don't always work well in a gravity feed situation.

Hmm. Maybe I'll fit a proper bike filter then.

cheers.

Remove the filter altogether as you do not need it. Make sure your tank is clean and use a reputable fuel station.
I had similar problem until I removed filters as told by bike mechanic now good all the way.