Taking clones now isn't going to make the clones crappy for evermore; if they survive at all they should be able to recover.
Re-pot promptly, bring that plant back to health, and then take cuts.
With a 2-3 foot plant, you have no choice but to run HID lights. Light penetration with flouros is less than a foot. MH in veg (that is what you have right now) and HPS for flower.
Read the link in my sig, then read it again. It will point you in the right direction.