My question is that if on a FREE HIT a batsman gets and inside edge and ball hits the stumps, can he take runs on that ball?
As you cannot be out bowled from a free hit you may score runs as the ball has not become dead. The same would happen if the batsmen was caught any and all runs are scored regardless of the catch.
The free hit Regulation is here
24.2 Free Hit after a foot-fault no ball... the delivery following a no ball called for a foot fault (Law 24.5) shall be a free hit for whichever batsman is facing it. If the delivery for the free hit is not a legitimate delivery (any kind of no ball or a wide ball) then the next delivery will become a free hit for whichever batsman is facing it.
For any free hit, the striker can be dismissed only under the circumstances that apply for a no ball, even if the delivery for the free hit is called wide ball.
Field changes are not permitted for free hit deliveries unless there is a change of striker (the provisions of clause 41.2 shall apply).
The umpires will signal a free hit by (after the normal No Ball signal) extending one arm straight upwards and moving it in a circular motion.
So you would apply the same process as for a no ball, and dead ball. So while the ball is not dead the batsmen may score runs.