My dual-batt setup consists of the following (see more details on my ROTW):
Hellroaring Isolator
Optima Blue Top in primary battery position
Slee washer bottle relocation kit
Factory battery tray (for earlier FJ 80) for passenger side
Mean Green "Hi Output" Alternator
I went with the Optima blue top for its deep cycle / starting capabiltiy and for its terminal configuration (top posts and marine accessory posts). The isolator is mounted on an open/flat spot high up on the firewall. The second battery gets very little use (only emergency starting when the primary batt is low) so any standard starting battery will work fine.
The Hellroaring isolator works GREAT. I would do the exact same setup again. The isolator is totally automatic and the LED indicator light gives you instant diagnostics of your charging system at all times. If the light goes out when the motor is running, you are exceeding your alternator output (either due to high load ie winching, lights, etc or an alternator problem) and the isolator has separated the batteries to protect your 2nd battery.
The Mean Green alternator on the other hand is a complete waste of money. It does NOT put out any more current than the factory alternator. That company completely LIES on their spec sheet and should be ashamed of themselves
Overall, the dual battery system is a must have. With an automatic transmission, if you accidently run the battery down (or have an alternator problem) out in the middle of nowhere, your gonna be walkin'!