I have the Fender Vintage Noiseless Pickup Set in my Standard MIM Strat. I really like the tone out of these pickups, but they are far too sharp, and they get a really bad edge to them when trying to get a fair amount of gain (think Clapton "Sunshine of Your Love" on 24 Nights).

I am using the included 1 Meg pots, would it be ok to run the pickups with my stock 250k Pots? Im not that electronic savvy, but im not a noob with it either. Im pretty sure I would be fine and wouldn't short/ wreck anything by doing so, but want to be sure.

I have also heard that pickup height is very important for these pickups, what should I have them set at?

Thanks in advance
i'd start by adjusting the height of the pickups, first.
height has a definite affect on tone, as well as output level.

go here:
and scroll down to the part about pickups, near the bottom of the page.

you can use your original 250k pots with no risk of damage,
this will take the edge off, but perhaps too much.
if they sound too dull with the 250k pots, buy some 500k pots.
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I installed the 250k and they are too dull.

Im going to GC to get 2 - 500k pots and a TBX, then I should be good.

I wont be getting the 500k's until next weekend.

The 250k's definately take out the sharpness, and they sound good, but it lost a lot of bass response.

I dont know if Im going to put the TBX in after all, at least for now Im going to hold off on it, I will put the 500k's in for now until I can get my hands on the Fender Mid Boost (Im basically building a Clapton Signature Model but with a different neck and trem style).
I got my 500k Pots ahead of schedule, I went today and got 3 Dime Size Proline 500k Pots. I installed them and gave it a brief test, and it sounded great. It gave a lot better single coil tone than either the 1m or the 250k pots.

I was very impressed with how it gave definition to the tone without beign too harsh. I definately recomend using 500k pots with the Vintage Noiseless Pickups.