I've done a 1FZ and 2 LQ4 45s.
the 1FZ is a giant pain in the ass for very little gain except that it's Toyota and it feels right with a straight 6. Other than that it has the horsepower of a 4cyl Camry and the wiring harness is fully integrated with the 80s harness. that being said, if I had to stay all Toyota I'd do the 1FZ again over a 1UZ or 2UZ. Ive talked with Toyota engineers about the 3UR. It's pretty impossible without a stand alone engine controller. It's also a very big engine. the dual overhead cams make it very wide on top. A 1GR would be a good choice too. Good power and size. Excellent engine, but I'm afraid the PCM would by unhappy in a retrofit. Almost better to put that Aqualu tub on the FJC chassis with the 80 axles and front links.
LS motors are very simple, very tunable, tons of aftermarket, built to be retrofitted into other things, and are reliable 300,000 mile motors. They are also very over used. Everybody's got one. For good reason, but still its nice to have something unique. The 4L80e and 6L65e are good, proven transmissions with lots of transfer case/ adapter options.
Duramax is huge. The Allison 1000 is also huge. The 6BT is also huge and heavy, and tall. The 4BT is heavy, gutless and tall. GM 6.2 and 6.5 are easy but not worth the trouble. I've done one of those too.