Before replacing the ECU try running a full tank of gas and check your mileage as it sounds like the tune up might have helped it run a great deal better and if I'm reading it right it sounds like the V-tec problem you are having is only going to show it's self when you are trying to merge in heavy trafic or other times that you want a bit higher reves and more power, thus it might be a non issue 99% of the time.
Also if it is the ECU it looks like you can buy a brand new one for $642
Honda Automotive Parts
Prices for stuff like that from the dealer can vary a great deal so I find it best to look at online dealerships to find easy to ship dealer only parts.