Am I correct in assuming these two will not play nice together at the range 1-2. Meaning if my Punisher with FCS attacks someone at range 2 I wouldn't be able to get the free TL due to the scanners correct?

Correct. LRS means you cannot acquire TLs on ships at range 2 or less from you, no matter the source of the ability to do so.

If you were passed a blue token for a ship that close to you, you would be able to accept it however, as that's not acquiring a TL.

Awesome, thanks