1999 cobra headers

I would go with BBK ceramic coated 1 5/8 longtubes. They will give you more power than shorties, but they are harded to install. 1 3/4 might be overkill. JBA and SLP are a little better quality but I didn't see any listed for your year cobra. Mac headers might be o.k. too, but I gave up on that company after the H-pipe I bought from them was a poor fit and needed to be bended. needles to say I was not happy after spending $130+. I threw that junk away and stuck with bbk ever since. I have been happy with my BBK products. As far as how much power they will ad, I couldn't tell you because I did my headers and gears at the same time. Should be a decent gain judging by the rest of your mods.

+1 on BBK. I have them on my 96 Cobra. They make the most power, they have a great fitment and finish. DO NOT BUY MAC!!!!!!!!!!!!!!!!!!!!!! They scavange too much and they will pull the valve seals from your car and it will burn oil and smoke. They also have slag from poor welds in the inside that get into the motor and cause damage. It is NOT worth saving a couple hundred bucks.

I would highly recommend a clutch install before you do the L/T's. I say this because they have to come back off to get the trans out doubling the cost of a clutch job. Maybe have them done at the same time. I had my new trans/clutch and longtubes done all at once, and I save big time labor charges. MY car had 40K on it and I had no problems with the clutch, but I'm sure I have won in the long haul.