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The first step in diagnosing this problem it to check for HVAC and Body codes. DO you have that capability?
With the scanner I use at my shop, I can monitor transmission shaft speeds for unwanted slippage. You'll need a scanner that can monitor live data stream for the PCM and use the transmission drop down / heading.
Check for voltage at the bulb's connectors. I've seen the headlamp relays fail on these vans. It could have a head lamp switch failure also. You'll need to follow the wiring diagram and determine where the car is losing power or ground signal.
What code are you getting. P0135 B1S1 o2 sensor heater failure?
I've replaced them before on the Sequoia. I've never had any problems afterwards so I'd suspect the actualotr or lock is aligned incorrectly. Pull the hatch panel off again and inspect the operation for free movement and alignment.
The best solution I've found is to use the pellet type bait poison. Place it outside of the car near the wheel well areas. Make sure no pets are around. They may be attracted to the poison as well.
you're having an immobilizer system problem. The small battery you're describing is not the problem. The immobilzer system needs to be checked with Honda HDS type software and compatible hardware. I've also seen high resistance at the ground G101 cause this issue.
EGR voltage at idle should not be higher than 1.21v. If it is inspect the egr sytem further. The idle may just need to be re-learned which is done by letting the car idle with no electrical loads on. Let the car idle until the cooling fans cycle two times. If there is an idle control system failure the car will typically code for P0505 idle control system failure.
2000-3000$ here in Raleigh, NC
It's common for the thermostats to stick in the open position on these engines. Remove the thermostat and inspect it.