Headers and a free flow filter - - well, I have a free flow filter - and I have not put headers on *yet*. I put the K&N Filtercharger on - it was NOT worth the money, I should have just put in a drop in - I think the results would have been the same. It did make a difference - but not like "hey watch this".
The results for headers and exhaust have been a little mixed - overall it seems as tho you get a little better performance - but there are a lot of hassles with headers. Downey and NWOR are the only two companies that make aftermarket headers for the 3.slow. While I have personally never dealt with NWOR - the general feeling is that they are not the best/easiest company to deal with. Now Downey on the other hand has better 'reviews' BUT the headers require quite a bit of fab on your part. It seems univerally accepted that you should put a 1inch body lift on your 4runner (the one size fits all syndrom) and then you will have to do some grinding and bending of tubing to get them hooked up and to fit in the engine bay. Otherwise you will have to hammer out you floor pan - - - wont fit around the alternator mount - -
There has been a discussion elsewhere that the 2 1/4 exhaust is right for the 3.slow - to keep the back pressure right - but Tim @ DOA racing (really good guy) swears up and down 2 1/2 is the way. Several really good suggestions I have(am) considering are to use the stock manifolds - move the crossover pipe out of the back of the engine bay and down. Then do a 2 1/2 cat back exhaust. This is in the works as I have welded the pipe from the cat back for a second time. Am I cheap or what

Oh well, this is what I was waiting for - and now the time has come. Do some experimenting - and if it does or does not lead to headers - I will already have the parts in place (i.e. already spent some money so the next chunk doesn't look as big)
As I said in another post - the 3.slow just doesn't seem to react great to mods. I have spent quite a bit of time researching it as my 200K mile truck is ready for some serious work. They do help - so far mine have made a positive difference - but it is not like other motors that can really jump to life with simple additions. This is why I just haven't jumped in and modded everything in sight - - the $$ per HP gain is just not very good.
As always - This is just what I have found thru A LOT of research and conversations/emails with people whom have done these mods to their 4runners. So I am not the end all answer - just realizing that the 3.0 is what it is.
Aaron