Hi Rasika,
As the gross salary is at Rs.20,000/- you could please check if your company has to enable any ESI benefit for the employee under the ESI act, because under ESI coverage if the employee's monthly gross salary is at Rs.21,000/- or less, then mandatorily there would be employee (1% of gross) and employer ESI contributions (4%).
You need to check on PF coverage as well for the employee ( calculated at 12% on basic and other allowances if the basic salary is less than Rs.15,000/- per month ) and employer contributions (8.33%(EPS) + 3.67%(EPF)).
The basic can be at any %. But the HRA for tax exemption calculations could be set 40% of the basic salary if the employee works in a non-metro city and at 50% of the basic if the employee works at a metro city.
By medical reimbursement, I believe you would be referring to the medical allowance component to be added to the salary stack. The medical allowance and conveyance allowance would no longer be required, as there is now the standard deduction of Rs.40,000/- per annum for tax exemption.
If you are referring to medical reimbursement where you actually provide reimbursement based on medical bills provided by the employees, then you can add this in the CTC component.
For adding the LTA component, there is no fixed percentage for this.
Hope these details provide a bit of an idea on the stack.