I put in synchromesh today in my car, and the transmission feels great so far, however, I have one quick question.

When I was putting it in, some came out, I'm guessing I got around 2.5-2.7 quarts in there (at most), and I read the maintenance guide, stating that a drain and fill uses 2.8 quarts. Will I be ok being slightly short on fluid?

You're supposed to fill it until it starts to pour out. So it sounds like you did the job correctly.

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Yeah, it was definitely pouring out abit, cool deal.

Also, how long will it be until I can feel the synchromesh "work its magic" on my transmission?

I have syncromesh in my car didn't cure my 3rd gear grind or anything to me its just tranny fluid....