The remaining work I did relocated the auxiliary battery back from the truck bed to the engine bay and ran new wires from the primary battery to the auxiliary battery and the auxiliary battery to the amplifier for the audio system. I also added new circuit breakers in those segments so that I didn't have to replace fuses if a circuit was faulty. Additionally, I added a new battery isolator for the aux battery. The original one I had was ruined when I overtightened one of the charging terminals on it, so I bought a smaller one made by Blue Sea Systems. Blue Sea makes some good products and a lot of other enthusiasts on the Tacoma forums recommend their products.
The other major part of this project I had to completely re-architect was the intake system. The reason for this is because the intake filter on the existing K&N system I had was in the way of the only available space for me to install the auxiliary battery. I cut it in segments and reinstalled with Specter Performance intake components from the auto parts stores, and in theory it should have worked fine. Their parts are modular and allow you to build your own custom intake system, but anytime you have a modular intake system, you have gaps. The gaps are sealed by using their silicone couplers, which are secured with hose clamps. This means a greater chance for air leaks exist.
Air leaks in an intake system are bad with fuel injection systems. The system is constantly monitoring the intake with sensors and if the air flow rate varies anywhere in the system, the ECU alerts you with a check engine light. That means your emissions will also fail if tested, and your fuel economy usually gets worse. Well, my check engine light came on because there was an air leak in the system. The AF ratio, or air to fuel ratio should be 14.5:1, or 14.5 parts air, to one part fuel. Mine was much higher in regards to air. To compensate, the ECU was dumping more fuel into the combustion chamber which meant, my fuel economy got worse.
I knew this because I have an inexpensive Bluetooth OBD II scanner that allows me to monitor my engine in real time while driving with an app on my Android phone. One thing to look for is the long term fuel trims; which shouldn't be more than +10%. See the image below, this is an actual screenshot of my truck while driving. Its +37.5!
I managed to finally fix the problem but it took forever. I had to remove the intake system and reinstall it several times until I got it right. But one benefit about doing all of this was it allowed me to reroute the intake tube back to the right front fender port where the factory cold air intake used to attach to. That's better because it draws colder air from the fender, rather than the engine bay where the air is warmer. Two images below show the K&N intake I had before and the modular intake I installed recently.
This image is from last year, and the K&N system worked great. Problem was it obstructed the area I wanted to install the auxiliary battery.
The image directly below is the intake system I installed from Specter Performance parts and the K&N kit
The yellow battery visible above is actually the original battery I had installed about 6 years ago in 2011. Its a Optima Yellow Top, and yes its 6 years old and still retains a charge. Visible on the battery mount is the Blue Sea battery isolator; it combines both batteries when the engine is running, and isolates them when the engine is off so that accessories only draw from the auxiliary battery to prevent from running down the primary battery.I've inserted some more images below of the wire and cable work. I also added some rubber diamond tread matting against the firewall to cover up all of the holes I drilled during the work, and to prevent inadvertent grounding of positive electrical wires.
When I finished I also decided to replace the spark plugs since the engine had been running lean for a while. I'm familiar with spark plug conditions, and I knew right away it had gotten very lean and hot in the combustion chamber. The electrodes are white and glazed with yellow, which happens when it gets hot very fast. I replaced them with new NGK plugs and so far things are good.
Specter Performance probably makes some decent accessories and parts for your vehicle, but I would not recommend their intake components under any circumstances. With the K&N kit, I never had any problems with it since it was engineered and specifically designed for my vehicle, and was a solid piece of tubing. These modular kits only invite problems to occur, and I've had numerous problems, even as recently as yesterday. I you are considering modifying your own intake such as replacing your factory intake with a K&N kit or any other aftermarket kit; don't. Your vehicle's manufacturer spent millions of R&D, don't mess with it.