A reflash will set you back around £350 but from all accounts your bike will run perfect from then on.
Why is this so expensive and why cant it be done with a laptop..? or failing that cant a 2007 ECU be sourced from the eBay / part-finder for less than that..?
It technically could be done with a laptop and the right software but you'd be stabbing in the dark without the dyno runs to give you the right feedback. It'd be like doing a custom power commander map yourself.... but a lot more dangerous for the bike.
It's more than just fixing the on/off fuel problem; the ecu controls everything so you can find tune every aspect of the bikes running.
Remove gear limiters, fine tune fuelling (without a pc3 or pc5), advance the timing, lower the fan temp etc
There's a lot to it and it's done wrong it can completely destroy your engine.
As for fitting a later ecu, a few people fitted the 2010 as that apparently has the best Yamaha map on it; I think it doesn't help the fuel problem but not as much as a custom flash would.
I also don't know how it works with regard to the immobilizer etc because I may be wrong but I think your key is coded to the ecu?