FE/FC FE501 stock exhaust

It has to -you're completely removing that welded in screen for a much more open design. I just put the Bds on my new 500exc, along with the jd tuner and zipty waterless coolant. Haven't had a Chance to try it out yet except for riding around the neighborhood. It definitely ran really hot before so I hope this cures it.

I already removed that outermost 'sink strainer' screen and it does help, but not as much as I'd like to see. Bike is still very restrictive feeling and HOT....even with the TPS bumped and JD tuner sending lots of fuel. It's just a very restrictive exhaust and am wondering if the end cap really makes a difference or not. thanks!

You need to pull the muffler apart as there is another one inside it!!! Have a look with a torch light.
Just removing the end cap doesn't do much with the other one still inside.
It's a double cone shaped mesh, to remove it do as follows. (can't believe no one on here knows this.... my dealer actually told me to remove it)
Take of the muffler.
Wear rubber or nitrile gloves and a mask as fiberglass is bad for your lungs and hard to get out of your skin!!
Undo the bolts holding the cap on and pull it apart. The perforated pipe in the middle is where you need to get to.
Where the weld is that hold the cone mesh is make a small cut with a grinder or saw to break the weld.
Wack the stupid thing out with a piece of pipe or similar.
Assemble back together. The quicker you do this from new the better as the fiberglass is packed in a plastic wrapper, if it's still there it holds it together.

Once this crap is out the exhaust is not very restrictive at all!
Take the mesh out of the air filter support too for more oomph or get a 2 stroke one, they don't have the mesh. ($20 bucks or something)

I'd drop the TPS back down to stock levels and add fuel with your tuner. Advancing the tps, advances the timing. This will aid to making your bike run really hot and could lead to failure.