Are you going to use one of the available swap kits for the Samurai?
I think we need to consider what this engine is going into, and what it's usage will be like. Will this be a strictly off road vehicle or a daily with some off road. What are you going to run for tires and axles, stock, 33"s or 36"? If you are going to go rock crawling you need lots of low end, mudding needs rpm's. You gonna run a winch? Need a bigger alt? Etc, etc. You planning on taking this through water crossings? All this makes a big difference in how you set up your engine.
Rebuid the 11 mm pump, have the bore checked and rebore if necessary, fresh bearings, gaskets, etc. and a good tune reflash. Best thing to do is contact a tuner you like and see what they say about turbos. Some require a bigger turbo with nozzles. Rocket chip has staged tunes that take you into the realm of turbo upgrades. Ask them about reliability issues with increased power and figure out how much risk you want to take. That's what I'd do, personally.