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Finally all stars aligned to make it possible for me, my wife and some friends to be able to take a drive to KY form NY for a quick Bourbon Trail visit next weekend.
Given that we only have 2 days to spend in KY we will only be able to visit 3-4 distilleries in addition to some other sightseeing friends/wife wanna do.

I've read a bunch of reviews and tips which help as far as picking out which distilleries to skip (given the time frame) but still don't have an answer to my question:

Which distilleries offer rare/hard to find bottles to purchase at gift shop and which do not?

There's a good variety of high end bourbon in NY but lots of stuff is still nowhere to be found. Not at fair price tag at least. I don't mind paying $100-$200-$300 as long as it's really that bottle that's worth it (yes, i know i know - a lot of people would never pay that for any bottle don't matter what it is, let's just say money vs taste vs what u thing is "worth it" vs something we call "individual basis" differs from one person to another)

Also - Are there any stores that are known for hard to find/rare bottles at decent prices? Would that be a better option?

Skip Four Roses, Woodford Reserve, and Buffalo Trace. Last year none of them had any special bottles of bourbon available. Buffalo Trace did have a special bottle of Vodka available at the gift shop but of course no special bourbon.
I think Heaven Hill, Jim Beam, and Maker's Mark all have special bottles of bourbon available only at the distillery.
Not sure about Wild Turkey.
Liquor Barn is one of the largest liquor store chains in Kentucky and they have a pretty good selection.
Good luck and have fun!

I recommend going to Bardstown. You can see Beam and Heaven Hill from there as well as Makers Mark if you want. The Heaven Hill Heritage Center usually has some rare hard to find stuff that is priced from $75- $500.

Beam has a new hospitality house that is supposed to be real nice.

Don't know if Barton Brands in Bardstown hosts guests. They make the 1792 bourbon that is pretty good.

Bardstown is an awesome town for bourbon enthusiasts and there is a nice bourbon museum that I recommend, as well as a bourbon bar downtown.

HH had a 13 year in a little ceramic jug when I went in 2011, it was good. Buffalo Trace was a great tour if you don't get hung up on lack of special bottles. Wild Turkey just had bottle engraving, nothing special in the shop (but Jimmy Russell was there that day!)

that's all I got, and definitely hit some of the local big chains!

while youre here, drop $100 and take a case of HH 6 year BIB white label home with you.

you can thank me later....

You might want to call Heaven Hill's visitor center (502-337-1000) and book their "Connoisseur Tasting". I did it a few weeks ago and for $25 you got to taste Larceny, an 11 yr old William Heaven Hill, Heaven Hill Select Stock and Elijah Craig 23yr. They're small pours, but it's a chance to try before you buy and you get to keep the glass. I believe the two Heaven Hill selections are available only at the visitor's center. They don't normally take reservations, but we were fortunate and they held 4 spots for us.

I'd also call Four Rose's (502-839-2655) and ask what bottles they have in the gift shop as it constantly changes, with private selections from Jim Rutledge sometimes being available.

Enjoy your trip!

Thank you for your feedback guys. In return here's a quick notes about my trip.

Overall I loved it and will be back at some point to visit rest of distilleries, more bars and more nightlife. Defiantly worth the trip and a quick "get a way"

Prices on bourbons at liquor stores are (surprisingly to me) a bit higher than in Brooklyn, NY stores. I figured it should be the other way around
but when it comes to pricier and rare stuff prices are a bit cheaper and there's more of that rare stuff available on the shelves. Not by much thou.
As for prices at distilleries - they are even more expensive that KY stores. Typical gift shop pricing where every t-shirt/glass/swag costs more than you can purchase them at other places.

We visited Woodford, Buffalo, Maker's Mark and Heaven Hill.

Out of these 4 HH is defiantly the best when it comes to bottles availability including rare and expensive stuff. They also have pretty cool "information center" aka a room to walk around, read, get interesting info while you wait for your tour to start or to just kill time. From history to general info to nice liquor orientated decor. HH was our last stop so we took "Connoisseur Tasting" as opposed to a tour walking around the facility. Same drinks poured as mentioned by GaryV. I actually ended up buying a few of those bottles.

Buffalo Trace is also very cool (and HUUUUGE) and should be on everyone's "to visit" list. Great tour, very knowledgable staff and great tasting session where if you ask they will pour you as many drinks as you can drink as opposed to rest of the tastings we went to.

Woodford is a beautiful place in itself located in the middle of bunch of horse farms so even drive to the distillery is great eye candy.

Maker's Mark's visit was spoiled by heavy rain and tour guide that knew nothing about anything. Young girl that just stared working there so you can't really blame her but MM should spend some more time training new staff IMO. Location itself is beautiful with a bunch of perks and details that differ from the rest, wish it wasn't raining the whole time so we could walk around some.

Small side note - Louisville's bars have an awesome bourbon selection with most rare and expensive stuff available as well as lot of bourbon mixed drinks I've never heard of before and some of them were good enough for me to order for myself as opposed to my typical "neat"