Why Conan Shrank

[DKMaester]

Actually, I think I have the answer:  Someone switched the pills.

Certainly, whatever Vermouth used has been completed for decades (at least since before Jodie's father was killed) and Ai mentions the project Conan doesn't know he is involved in has been ongoing for 50 years.  So the organisation had the ability at the time, it just took someone to place a shrinking pill in Gin's batch of Apotoxin.

As for who...
It's pretty clear that Gin wasn't aware of it.
Sherry didn't work it out until the second investigation of Shinichi's house.  (So she probably knew there was a chance of survival when she took the pill.)
Vermouth has the motive but not the opportunity if she was in America at the time.
It was probably the as-yet-unknown Sherlock Holmes fan since this trick comes right out of A Study in Scarlet.  (Yusaku is the boss?)

What you're saying would mean that Shinichi was given the shrinking pill by chance. Gin could just as easily shot him or stabbed him. It was also by chance that Shinichi even followed Vodka and saw the deal going on. The only one I think could have switched the pill and given it specifically to Shinichi is Gin himself. And if Gin did that then the plot would definitely thicken.

[SkyVenger]

No, it's risky because when he uses a gun, it'd make noise; knives are ok though - he should've done it before instead of hitting him w/ a bat... or maybe he just doesn't bring one.

God, why did they even meet near a populous place (Tropical Land)? Hmm...

[Rio Nagava]

I think you missing the fact that drug - shrinking people is rare event. Ai said so. Sure it's not the greatest proof. But it could meant that Gin couldn't know that drug could shrink people. And not to mention that Gin brought this drug in special case. With not only pills, but the the liquid as well. Just enough for one person to take the pill. But i doubt that he meant this person to be Kudo.
It's seems odd.

[kkslider5552000]

it's a bizarre coincidence.

Since someone shrinking because of the side effect of a drug is pretty much the only thing except magicians (that I've seen) that isn't "realistic" in Detective Conan, there doesn't really need to be a logical reason why the main character shrank.