The alternator in a vehicle is not designed to fully charge a battery, compared to the charging system in a blue water sail boat, which might have 3 stage charging with battery and alternator temperature sensors and compensation algorithms. You can do what you can to help it out, with thicker, shorter charge wire but if the thicker wire is only between the isolator solenoid and second battery, and you are relying on the OEM wiring between alternator and engine battery, then 4/0 gauge will do nothing extra when wired between the isolator and second battery.
If you do not add thicker ground wires as well, then you will not increase the amps or current. Put a thick ground wire from alternator to the engine/ frame. Between battery and engine and frame, frame and engine. Give it multiple paths.
My Dodge Van has a 130 amp externally regulated alternator. I have seriously upgraded the charging circuit. I have 1 engine battery and 2 flooded true deep cycle house batteries 115 a/h each. I also have solar and a battery monitor which reads alternator amperage, and this tool has been a big eye opener.
My Voltage regulator is internal to the engine computer, but luckily it only throttles back the output after the batteries reach full charge, or once ~14.5 volts is met. The only other times the voltage is lower than 14.5, is at low rpm, with depleted batteries. Once it reaches 14.5 volts, the alternator only puts out enough amperage to hold that 14.5 volts. Unfortunately that amp number can be 15 amps despite my batteries being over 70 amps from full. So If I were to rely on the alternator to fully charge the batteries, I'm looking at close to 5 hours.
Even though my batteries could easily accept 40 amps, the alternator only needs to produce 15 to 20 amps, if that, to hold the 14.5 volts, so that is all it does. So my 130 amp alterantor is gonna need 5 hours of engine speeds above 1800 rpm to replace 70 amp hours into my batteries. It sucks, but that's the way it is, on my vehicle, on yours, and nearly every one out there.
I also suffer from despicable amperage at idle speeds when the alternator is hot. It simply cannot make more than 32 amps at idle speed when hot. If I have my high beams on, and blower motor on high, 10 amps are flowing
from my batteries. The alternator simply cannot make the amperage at low rpm to make enough current to keep the batteries up in the 14's. You cannot add more load to the alternator and expect it to charge your batteries any faster.
Since your Toyota's voltage regulator was designed to never go above 14, as soon as it sees 14 volts, it only allows the alternator to make enough current to keep this voltage, this your battery is never gonna fully charge via the alternator in any hour long drive. Not gonna happen.
Even if You got an alternator that is designed to make big amps at low rpm's, the limiting factor is the voltage regulator. Once that voltage setpoint is reached, it cuts the alternator down.
Basically you have few options Your 13.8 volts is the limiting factor.
You can add a voltage dropping Diode in the alternator sense wire, so the voltage regulator sees a lower voltage and allows the alternator to put out more amps at higher volts, but this only works with externally regulated alternators.
You can try adding a separately regulated alternator, but with a shared ground, things can get a little complicated.
You can try keeping the battery and alternator cooler. Most all computerized vehicles try to regulate battery charging voltages by temperature. The higher the temperature,the lower the charging voltage. It might have a battery temp sensor, or it might just guess using the coolant temp sensor or an ambient air temp sensor and a programmed algorithm.
Basically, whenever you deplete your batteries, when you get home, you need to top them off by plugging a charger into the grid. That helps keeps the batteries healthy, and reduced stress on your charging system.
My engine idles so much smoother when the alternator only has to add 2 amps into the batteries, instead of 32. It takes 1 HP for the alternator to produce 25 amps. It is not free electricity.
Here is a link to a chart showing how much better a 120 degree alternator performs than a 190 degree alternator.
http://www.betamarinewest.com/balmar/6-series-sheet-web.pdf
You can also see how some of the lower amp alternators produce more amps at lower rpms than the higher amp alternators. Keep in mind, these are the Balmar alternators, pretty much the top dog in the blue water sailboat world, where they need to reliably recharge a large bank of batteries as quickly as possible at lower rpms. They perform way better than a vehicle alternator/ charging system that was designed to top off a small, single, slightly depleted starting battery.