It appears that I have tuned my engine to the point of starving itself of fuel. At higher speeds, the flow into the carbs isn't enough to replace what is being sucked out of them.

Found this out today by thinking i had blown the engine. It spluttered, coughed and started running on 1 cylinder. when I backed off it ran fine again after a few seconds. Opened it up and it went again, few seconds later, same thing happened.

Are there any upgraded fuel system components available, or anything from other bikes that fit?

Cheers.

What year is your bike?  There's a well-documented frame petcock vacuum issue.  It affects all pre-2001 models I think.  I have a '98 and definitely have the petcock fuel starvation issue.  Running it with the frame petcock set to prime works for me though.  Try that, if that doesn't work, it's probably something else.

Mines a 2007 model.

I am considering using the fuel system off an NTV 650, as they use a fuel pump and that should keep the carbs filled up 

The standard fuel system will do the job fine on an '07, as long as its all working.
1. Check the vent in the cap is clear (after you get the problem, open the fuel cap and see if there's a vacuum in the tank)
2. Check the fuel strainer in the tank is clean (part of the tank petcock).
3. Check fuel lines are clean.
4. Check vacuum hose to petcock.
5. Check petcock.

There are instructions on here about how to make your vacuum petcock into a manual one if that is the problem.
There is absolutely no need to invest in the expense and complication of a fuel pump.

good lord, we're talking about a parallel twin here, definitely no need for a fuel pump.

put it on prime, if that fixes it then either; your low on fuel (prime runs off the reserve) or the petcock is bad or the vacuum line to the petcock is blocked/torn/not-installed.

if that doesnt fix it then check the tank vent (could be clogged), the tank petcock(slot should be vertical), and carb vents(could be clogged.

I've had fuel starvation problems on & off on my 97. Replaced the petcock a couple of years ago, and have only had the problem once since then. The problem turned out to be the routing of the fuel line from the petcock to the carbs. The line got pinched at one point, restricting the fuel flow to where it couldn't quite keep up at freeway speeds.

Same thing also happens if you put the float bowls back on backwards.
Not that I've done that or anything...