I have a 99 with the 4.0 ohv it has the muffler removed already and I was wondering if adding aftermarket headers will decrease my low end torque. I also have a k&n air filter

 

Factory exhaust is tuned for mid-range power.

Tuning an exhaust system is done by creating a velocity and suction in a specific RPM range, this causes negative pressure at the exhaust valves to pull out exhaust better in that RPM range, so increasing performance, in that range.

Headers can be designed to change this range lower or higher, they don't add power just change when the highest negative pressure occurs in the RPM range.

The myth of "back pressure" comes from this tuning, people would slap on bigger pipes and lose power, "WTF??, I guess engines need back pressure from smaller pipes"
Nope, what they did with the larger pipes is to lose the velocity in the system so they reduced or eliminated the negative pressure at the exhaust valves that was increasing the performance.

I am not an exhaust designer, above my pay grade, lol
But with the right headers you can lower the RPM range where you get the highest negative pressure, giving you better acceleration, but you lose it at the top end

 

I have found most headers are designed to improve horse power at higher rpm and typically give a reduction in low end torque.

The headers I have experience with did cause a loss of low end torque. I was so happy in one case when the headers cracked after a few years of use. I put the original exhaust manifold back on an got the low end torque back. That was on a 73 Landcruiser and was not a high rpm engine. It worked much better off-road with the stock manifold.

I am not saying headers are not good. You just have to know what they were designed for and make sure the engine will be happy with it.

BTW, RonD is right on with his explanation. Most people don't understand the true mechanisms of headers.