Surely it would be cheaper to ship USA to USA than Canada to USA? Or was your buyer in Canada?
Why did you pay customs on the item? It was your property until it was paid for, wasn't it? Or were you obviously bringing a bunch of parcels into the States? The US customs people would get officious about that.
Frankly, it sounds like you communicated too much. In hindsight a note that shipping was less than you expected and here is a partial refund, with no more comment than that, might have been better received. (and there is a lot to be said for Paypal's "stealth" shipping labels.)
So now i got an email saying i m going to leave negative feedback, if u dont refund me.
Well that's a good thing. If he actually follows through, that threat could be enough to get his feedback removed.