Honestly you have to go deep if you want to run with the big boys and I'm talking 200-300 feet, as stroker/big bores don't add top speed they add acceleration. Head work, jets, and a pipe aren't what I would say going to give you what your looking for.. That would maybe be a 25% increase over stock. You need more displacement as most of those new quads are 700cc plus and have stock (HP)what all modded stroked out big bored 350 would have.
The stock CDI box has no rev limiter.. basically you rev it until the valves float, and really there is no power up there anyway so there is no sense to reving the engine that hard. I have a dynatek for mine and yes it does add a little snap but I wouldn't call a worth it for the money upgrade.
As far as this holding up, I don't see it being a problem as long as you change the oil and run a good oil cooler.

 

Thanks, might go .30 over...