Its not a 4Runner but hopefully it gives you some ideas.
I have both a Yaesu FT7800R and a Uniden CB on this truck. Having the Ham radio is great, but not if everyone else has only CB so I just use both. I am really picky about clean installs so I took my time with figuring out the best place to put everything.
The Yaesu has the remote kit, which allowed me to mount the actual radio under the passenger seat. The speaker for it is mounted to the bottom of the CB radio. I used to go without the external speaker but it was hard to hear the muffled audio from under the seat.
For antennas I have two NMO mounts on the roof. For daily use I have a short Larsen dual band antenna and leave the CB mount capped.The picture with both antennas is how I setup for trips. Its a Larsen NMO2/70 and a Browning CB antenna (I now have the matching black Larsen CB). While I cringed about the prospect of drilling into the roof at first, I realized that it is hands down the most professional, clean, waterproof, and best looking way to go. The performance of the antennas on the roof is fantastic. Having a good ground plane is invaluable for antenna performance.
I hope this helps!