I have a 01 accord EX (v6, 6cyl, 3.0)
So I’ve found 3 exhaust systems,
invida, magnaflow and apexi.
I know I don’t want the invida because I heard it’s very loud and sounds kinda ricey. The apexi I heard is very quite and for that price of around $900 not sure if I’d want that. The magnaflow from what I’ve seen sounds decent.
Is there any other options I could look into getting or doing?

 

this kit I know bigger and more shiny is better... but i recommend the 2.5" aluminized steel (unless you live in the snow belt). you'll save $175 and won't notice the difference.
plus two of these same quality and construction as Magnaflow but less expensive (virtually zero marketing budget to support)
resonator: you can add one with the tubing kit or order one with the mufflers. either way, it probably sounds better with one.

if you don't have the ability to weld it yourself, your local muffler shop can take care of it for a nominal fee.

excluding shipping and the muffler shop fee, less than $300 for a very functional sports exhaust.

 

So I’m currently running the apexi ws2 on my v6 01 accord ex. Looking to find headers that would be compatible with this exhaust syestem.

 

Didn't think Apexi made a bolt in kit. If it isn't and it's custom, then you are kinda on your own with anything fitting like factory.
Most V6/downpipe kits I see for the J30s are usually made to fit in the same place as the factory bits. So if your exhaust mimics the factory pieces, up to the factory down-pipe before the catalyst, they you may be OK.
Welcome to the performance aftermarket, where things look like they will fit and lots of times they don't.

 

The header's need to:
a) have the right engine end flange for your engine (Correct mounting hole size and location, correct exhaust port size and location)
b) have the correct bends for your engine bay, your engine and the particular layout of your car as well as for the final placement of the discharge end of the header
c) have the correct discharge flange that bolts correctly to your catalytic converter or cat-back exhaust

If you have an A'PEXi WS2 muffler and thats how your determining that you have an A'PEXi WS2 cat-back then you may just have a WS2 muffler on a factory Honda cat-back because A'PEXi did not make a cat-back for the '01 V6 Accord, only the '98-'02 4cyl's w/ the F23 engine.

Get under there and take some pictures, because either:
a) you have a completely stock exhaust aside from auniversal WS2 muffler
b) you have a A'PEXi WS2 cat-back that has been modified to fit your car
c) you have a cat-back that looks like an A'PEXi WS2 but isn't and is made by another company (Don't worry we can still get you a header as long as its a cat back for your make/model/year/engine)

It's important because we need to know if your pursuit of an aftermarket header is for a car with it's cat in the original factory position, it determines whether its gonna fit at all. If you have a modified exhaust and your unsure of what it is, take pics, mainly of the cat, where it connects to the cat-back and where the header connects to the cat.

 

Once we determine is your cat and its inlet flange are in the oem location...
Here are some options for headers for your '01 V6 Accord:


*Best option in terms of effectiveness and final price.
DC Sports HHC5528 Ceramic Header - $366.67

*Best option in terms of quality and performance.
(Made of stainless steel instead of ceramic coated mild steel, better welds and flanges, less likely to crack)
These two are used.
eBay - Used - Comptech Headers - #1 - $775
eBay - Used - Comptech Headers - #2 - $825

There are other options such as no-name eBay brands that will work and be fairly inexpensive but your taking a risk there.
Not sure if brands like OBX Racing, Megan or DNA Motoring make headers for the '98-'02 Accord V6 but I couldn't find any.