Another vote for the 3B. This is exactly what I am doing with my rusty BJ60 and a 109 5 door that I will be picking up soon. My 60 currently has a 4 speed but I would like to have a 5 speed. The 3B/5 speed is a long drivetrain and it may not fit too well in the 88" but just fine in a 109" For a 88", I would stick with a 4 speed.
My plan is a SOA 109" 5 door on FJ62 axles with a Toyota 3B/H55F 5 speed. I want a low SOA and 33" tires. I think this would be a really cool rig.
To me: I am combining the best of both worlds. I love both Cruisers and Rovers and to make a hybrid of the two is even better. A 109" with a Toyota diesel that can cruise 70 mph and get 20+ mpg is the ******** if you ask me.
Just my $.02