Graduate assistant with W2 and 1098-T scholarship how to get Lifetime Learning Credit

Son is a graduate assistant and employed by the University as asst football coach. W2:  wages $46,000; federal tax w/h $2,100; SS wages $11,700.  I knew right away they didn't take out enough fed withholding, even though he claimed 0 on his W4.  Why such a discrepancy on wages and SS wages?  No clue!  1098-T lines 1 and 5 are:  $7,700.  No other boxes.  He owes almost $2,000 to the IRS!!!  The $7,700 is all paid for by the University, who is his employer and as a grad asst must take Master's classes at least half time.  The software questions go like this: "What portion of the $7,700 is employer tuition assistance?" "Now tell us if you're including any of your REMAINING grants/scholarships in income?" "Why you might want to do this." In the past, I was told to add $4,000 to income, as it was the maximum to claim the LLC and it did lower the tax burden.  I'm still confused!  Is $4,000 the amount I add to his income? Please help me understand and tell me where to put the correct figures!  Thanks.