I have an '87 4Runner with the enemic 22RE with 220K miles on it.
I need to replace the manifold ( cracked ) and the exhaust ( holes ).
I replaced the cat about 2 years ago with a high flow unit, so that is still good.

Any real world experience with going with an upgraded header & higher flow muffler as opposed to stock?

A few more ponies will be great!

I tried looking for this type post, but could not find one. Might just be operator error on my part though

There's lots of headers for the 22R/RE. Doug Thorley is probably one of the better ones.

I have a NWOR try-y header on my 22R webered pickup. They are based in my town and used to have a storefront not far from my house so in the past I have been there quite a lot for bits and pieces. Lots of people rag on NWOR about the customer service but in person they were great. The header I have was purchased in 1998, and now has around 90,000 miles on it. It still looks and performs just as well as it did new, I don't forsee any failure there for another 10 or more years. That truck is still my favorite to drive around and it is nearly impossible for me to keep my foot out it every time I fire it up.
If you decide on a header you should at the same time upgrade to a 2 1/4" inch exhaust with a low restriction muffler. I bought the NWOR exhaust kit at the same time (no longer made that I can tell, I wanted another for the 4runner) as the header and have been nothing but pleased at the results.

I just got off the phone with NWOR, they have the headers I am looking for....for $519.

I am going to have to look and compare pricing...that is a lot of $$$.
Maybe that is normal though, I've never priced headers before.

Whoa, that sounds outrageous! You can get LC's headers for around $350 and they are 14 gauge stainless with ceramic coating. I know the NWOR headers are good as they were, maybe they upgraded them and they are worth the price?