"Does BOX 1,3, and 5 amount should be reported after subtracting employee contribution for 401K and HSA?"
No, only HSA (box 12, code W) is subtracted from W2 boxes 1, 3 and 5. A 401k contribution (box 12, code D) is subtracted from W2 box 1 only.
"Also, Does BOX 14 sould include both employee and employer contribution towards health plan?"
I expect it's employee contribution but you should ask your employer for this answer.
