Now because the tune disables VTCS, will that lower the life of the cats since they are not being warmed up the same on start up? Are their any issues that come along with not using VTCS?
Not really, no...although i didn't buy an MP3 or anything, but i don't think thats exactly what VTCS does anyway...
VTCS is basically an elaborate 'choke'...it uses butterflies to restrict air flow and cause turbulence right at the intake section of the head...which does two things, both giving the same result...
The restricted air flow automatically richens the mixture WITHOUT adding more fuel, the holy grail of cold start emissions...you get a nice rich mixture that burns very slowly and evenly heats up the combustion chambers...but unlike the standard protocol for this (dumping in fuel), the computer can use the same fuel mapping as if the engine was fully heated already...
the other effect is the turbulence the system creates...It spins and throws the air around, which allows it to mix more thoroughly with the gasoline being injected...it also helps reduce gasoline condensation on the ice cold cylinder walls...both of these bring the 3rd gen protege into U-LEV compliance...and thats about it...
The difference with the Mp3 ecu is that it doesn't have a protocol for cold starts that utilizes VTCS...it richens the mixture the old fashioned way (dumps in more fuel)...if anything, this will actually heat up the pre-cat faster than the VTCS system will...as more air is getting into the chambers, and more gasoline is being injected...so the overall intake charge is larger, and will heat everything up faster...although, its marginal...and not really noticeable to the driver...
so realistically...there will be no difference to pre-cat life...and actually, how quickly the cat is warmed up will have no real effect on its life cycle...cat temp only effects its ability to 'eat' unburned hydrocarbons...not really how long it lasts...
The only real issue between these ecu's and VTCS is when you remove or disable the system and still use a standard ecu...of which is looking for the VTCS, and providing fuel requirements as if the system works...if you do that, you most definitely WILL have some cold start trouble when the temps are very low...the mixture will be overly lean, and there will be noticeable hesitation at below freezing temps...after it finally warms up, everything will be normal...but its hard to say that setup is ideal for people that live in colder climates...