I bought my '91 with the 1.6L already installed in '07. This model has the fuel injection and it remains installed intact.
While 1.6L has more torque, it doesn't rev as good as a 1.3L. When I want to accelerate quickly or run on the interstate, it runs out of gearing real quick with near stock tires. Since mine is a daily driver and having kept the weight down, I wish it still had the 1.3L block in it. If I was running 31's, heavy bumpers, winch, etc, then the 1.6 would be the better choice.
It really depends on how you plan to use the truck. If it is going to so a lot of highway use with occasional trail action, I would rebuild the 1.3 and install high compression pistons.
Whether you go 1.3 or 1.6, you will need to replace the exhaust system, if it hasn't already been done. The stock exhaust is less than 1.5" and really needs to be 1.75" to 2".
The trouble with buying a used engine, is that you never know whether it needs to be rebuilt or not, unless you know the history of the motor. Seems like those that I hear about are worn out and being parted out. Here is a place in Lawrenceburg, TN
that I saw listed in the nashville.craigslist that has a lot of parts. Never dealt with them so I can't recommend them.
My mother lives in Murfreesboro and I get down there about one a week, mostly on the weekends. If you would like to get together in M'boro, just private message me and we can try to schedule a time and place. Always glad to meet another Samurai owner.