Problems at high speeds.

[mr self destruct]

I have the same down pipes on mine and it runs cleanly.
Did the issues come on suddenly or progressively?

Is the choke working correctly and the plungers seating properly when it is released.
This was the first thing I checked when it first happened on my sons bike because I had seen a similar problem on an old GS750 Suzuki when the plungers were not seating fully due to corrosion, a shot of WD40 sorted it out.
Have you checked all the usual items like wiring for corrosion.
Drain the float bowls to see if help first and then check the float heights using transparent fuel line.

It's difficult to say, in the decent I take the B road route to work where you can't really do more than 60, so it may have masked when the problem arose. It's only been over winter I've stuck to the motorways and noticed the problem.
As for the choke, this might sound odd but I've never touched it. No matter how cold it's been, the bike's always started and ran a treat if you don't count last year's plug cap issue.
I think some carb stripping is on the cards but I'll check the wiring out before that.