I'm starting to write riffs and chord patterns etc but I like to use less common chord shapes and stuff like that, but I really want to know what the chords I'm playing are so I can improve my theory prowess and work out keys for constructing solos.

The first chord I'm struggling with is 6th-mute 5th-9 4th-7 3rd-9 2nd-mute 1st-mute

So thats F#, A and E

Any ideas?
That's an A/F# chord.

As for identifying them by ear you just have to train it well, as with any other exercise which requires good ears.
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Hmm judging from your pic you'd fit in more with a fat busted tribute.
If you download the PowerTab program you can write it as a tab and then there is a chord indentifier which tells you what the chord is
Learn about chord construction. Look at the FAQ IN BIG WRITING AT THE TOP.
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Go to your staff paper and re-write this song a half step down so on the paper it'll be like you have a "C" just move it down to a "B#"

Know your theory, then play like you don't.

F#, A and E would be F#m7.
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Thanks ye I read through THE BIG FAQ AT THE TOP (patronising git) and found out its F#m7. Thanks for the conformation guys