Where does the amino acid at the acceptor stem of tRNA come from? Where are the amino acids synthesized, if not from the tRNA itself, and how does it make its way to the acceptor stem in the first place; what role specifically does the anticodon pairing play in this? And if it is synthesized from the tRNA, how does the tRNA remain unaltered afterwards, and how specifically does the anticodon pairing effect this?

Amino acids are synthesized from their own pathways, entirely separate from the synthesis of RNA.  A family of twenty aminoacyl tRNA synthetase enzymes is responsible for joining the amino acid to its cognate tRNA.  These are questions and topics that it takes a biochemistry textbook chapters to develop.  

40 minutes ago, BabcockHall said:

Amino acids are synthesized from their own pathways, entirely separate from the synthesis of RNA.  A family of twenty aminoacyl tRNA synthetase enzymes is responsible for joining the amino acid to its cognate tRNA.  These are questions and topics that it takes a biochemistry textbook chapters to develop.  

I see, thank you for explaining. Do you know of any sources which describe this process in optimal detail?

Nelson and Cox's Principles of Biochemistry.