Only way the wheel is related is if you have warped rotors pushing the pistons back in as the wheel turns. You'd know if that was the issue.
As for upgrades, the radial brembo from R6's is a fav for alot of people. The cbr went to a radial master in 07 although not brembo.

 

I'm fairly sure it's not related to the wheel as given how inconsistent this issue is surely if I had a wrapped rotors it would be happening more frequently.

I can get hold of a near new 2013 cbr 600rr front lever with mc, bracket and reservoir for a reasonable price, don't suppose you know if this will fit?

 

What's a reasonable price? Guys that swap the radial setup from an r1 on their 08+ cbr 1000rr say they notice a difference. I just scored a duc 1098 brembo master for $100 for my bike. Depending on the f4i caliper piston size, you may not want an 18mm master. It may be too big and not give you enough feel.

 

I just paid £100 the seller claims it's brand new, he took it off as he built a track bike and has loads of other rr bits for sale so seems pretty genuine. Got a pretty nice track bike for sale too.

CBR 600RR 2013 FRONT BRAKE MASTER CYLINDER | eBay

Didn't think that price was too bad? Just hope I get this issue sorted! On the plus side I will have rebuilt the calipers, ss lines and radial mc in the process.

 

Hard to go wrong. I guess I quite don't understand it being taken from a new bike, unless the brand new bike is being fitted with an aftermarket or something.

 

Yeah looking through the sellers other items the rr track bike has brembo brakes fitted which says it's only done 700 odd miles. We'll see how it goes when I get it fitted.

 

I'm sure you'll be pleased with it! Even if you had to make a new reservoir mount for it (in case it hit your top fairing), it's going to be a worthy modification.