Just a couple comments on a Whipple setup, The reason you see a loss with headers is due to the loss of scavenging and less velocity through the intake / head / exhaust system. Port the heads, change the floor level to increase the flow & velocity and the little 3.0 heads wake right up & now your headers help the situation as they are able to smooth & handle the increased air flow from the additional flow through the heads.
As for timing, even at 6 psi, with premium fuel, its going to knock/ping in the upper gears on stock tuning, you might get away with it in 1st gear maybe 2nd. A very general rule for tuning SC vehicle is to pull 1 deg of timing per lb of boost on a WOT top end pull, this is only a base starting point, of course your MAF signal is going to play into this as well on WOT and mid range. The Whipple kit added a 4.0 MAF as the 3.0 was easily maxed out with adding the SC & caused frightful lean spikes.
I have mine tuned to run 87 octane, & big shots of H20/Meth under boost, and its good most of the time, occasionally it will slightly knock depending on weather conditions & only on WOT in high gear, like a big top gear roll on.
Most of the time I run a 75% mix of 87 or 91 octane gas with 25% E-85 and it seems to like it really well, no knock and my mileage stays in the 16-17 mpg range as I do mostly city with just a short bit of highway driving.
The Whipple kit came with a 160 thermostat, I never had any luck as it caused the engine to run too rich all the time, Mine runs better on a 185 stat.
As for the Air cooler or Meth setup, an air cooler would be nice but it seems that the intake runners get way too long trying to hook everything up on the Ranger body. I have a dual shot meth setup on mine, I shoot before the SC and after, triggered by boost pressure, MAF signal & throttle position.
One thing you need to change is your air filter location, your not going to make HP on hot air and from the pics posted of the OP's setup that open filter is doing nothing but sucking in hot air, anything taken from under the hood is ridiculously hot after even a short drive.
I did a ton of work on my intake to get a good sized tube into the grill area from the stock air box and lid with a panel filter to get ambient air into the system, and it works, I generally see pre-SC intake temps 2-3 degrees below ambient temps, even a greater delta in the winter months, sometimes as much as 10 degrees below ambient. I am setup to see both pre & post SC temps in the cab on the Scangauge II.
Believe it or not the 3.0 is a great engine for boost if tuned correctly, 6 psi - better than stock but still pretty boring, 10 psi - runs decent, 15 psi - now you have a good v-8 killer, 17-18 psi is a torque monster that will just scream. 20 psi hauls the mail, but life can be short as it will eventually vent the head gaskets, and the rod bolts on these 3.0's are tiny and can be easily wadded up at this level.
My Experience: I have a Whipple, heavily modded 3.0, ported / polished heads, intake, upper & lower, roller rockers, bee hive valve springs, headers, running on ~18 psi with a 2 shot H20 / Meth setup, its my daily driver year round, yep even in the Indiana winters.
The whine is great, the HP and gas mileage are good too.
I applaud you on your efforts for the Eaton kits, keep working the bugs out, but whatever you do plan on tuning it accordingly, the H20/meth setup, polishing on the heads and air to air cooling are all just ice cream on the pie, while it may add flavor, its not going to cover up the bad taste of a poorly made pie.
JP02XLT