Hi seantreanor,
1) As these benefits are payrolled, you do not need to include them.
2) As the tax due on the disposal of your shares via SIP has already been paid via PAYE, you do not need to declare them.
more advice here:
Tax when you sell shares
3) For more advice on the Student Loans present in your tax calculation, please contact the Student Loans Company, here:
Contact SLC - repayment enquiries
Thank you.