Both are correct with different meaning. The perfect ( have uploaded) is for action completed in the present: I have uploaded the files, the job is done now. The pluperfect ( had uploaded) is used for action completed in the past: I had uploaded the files before you asked me to.
I have uploaded
Yes, the sentence "when he officially files leave of absence" is not grammatically correct. It should be "when he officially files for a leave of absence."
"Not like that" can be grammatically correct, depending on the context.
The phrase "Is you don't miss me do you" is not grammatically correct. It should be rephrased to something like "Don't you miss me?" to be correct.
Yes! That is grammatically correct!
Yes, 'for free', is grammatically correct.
The phrase "You are not knowing" is not grammatically correct. Instead, you can use "You do not know" or "You are not aware."
The Kindle can read PDF files uploaded from a USB memory stick.
'Once photos are uploaded' and 'once photos have been uploaded' are probably both correct, but I would use once photos have been uploaded
Yes, Almighty God is grammatically correct.
"That was wrong" is a grammatically correct sentence.
Yes, it is grammatically correct.
The sentence "Rhoda's Crazy" is not grammatically correct. It is missing a verb to make a complete sentence.