If I'm still working on my first play through, will my stats be uploaded or only after I beat the game? Also can I get the Gold Star achievement on my first campaign playthrough or does it only start counting 100%s during single missions?

Your stats will be uploaded anyway, if you're playing the game and connected to Xbox live. I think you may have to be signed up to the Social Club first though, I haven't looked to see if you can check your online stats in-game.

I don't think you get the option to replay missions until you've completed the story or fail a mission. I guess you could abuse the save system to reload when you don't get 100%. If you're planning on playing through the story at least twice though, I'd forget about the achievements for now, see what unlocks anyway and leave achievement hunting for a subsequent playthrough. I always find I enjoy a good game less if, I'm pre-occuppied with achievements.

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The tougher the battle, the sweeter the victory!!

It will count your stats during the first play through as long as you don't die, fail the mission, or take a taxi. Otherwise you'll get 0% and need to play that mission again after you beat the game (if you want the achievements anyway).
I'd suggest just playing through the first time and getting familiar with the missions since it's not likely that you're going to get 100% on the first try anyway. Once you know the mission and what's required, then it's easier to go back and focus on the objectives.

Btw, does anyone know if you have to do something special to get your base-jumping stats to record on the Social Club. I've completed the base-jumps in Free mode in under 8 minutes, at least 4 times and several times over 8 minutes. But, I still don't see my stats appearring. Apart from the 'your stats' section for GTA IV, which is completely messed up, all my other stats are correct. So, it's not a case of needing to relink my gamertag because, apart from those two sections, all my stats appear correct and up-to-date.

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The tougher the battle, the sweeter the victory!!