-Ford EFI (have heard they are less tempremenal, easy to tune, they just work)
Yes, but not with that cam they don't. You'd need a special tune at the very least. I have a hot-rodding buddy that had the choice of E303 or Explorer and he just couldn't fathom building something without going bigger for more fun factor.
Well, the fun factor wore off even for him literally in the first week.
And he DID like the idea of a hot rod. If that tells you anything.
-Thought of an NV 3550 5 speed would be best?
Hard to decide what's "best" for someone, but generally speaking they're a great transmission for your kind of Bronco. The newer AX-15 as well. They're both physically almost the same dimensions and the AX has a taller first gear so not quite as truck-oriented.
-33" tires (will be lifted 4.5 total, 1" bl plus 3.5 sl)
Popular setup. For a LUBR you could even go 3.5 total and keep it easier to get in and out of. You taking wives and kids around in it? Or all adults? And the spouse likes climbing and jumping? Some do, some don't. Which is why I ask.
A 16" tire with a narrower tread will be easier to fit on an uncut rear. Keep the wheel width to 7 if you can, and 8 only if you have to. Don't go over 8 inches wide. And watch the tire size and axle location. With a 33 you should at least plan ahead in case you need to move the axle back 1" or so to help the tires clear the leading edge of the uncut rear wheel well opening.
-Currently the truck has 3.50 gearing - no problem changing the gearing to what I should run.
Good. 4.11 minimum with a stock EFI engine. With the engine linked above I'd think 4.88's would be the ticket for happiness.
Let me clarify when I said I don't want a hot rod, I don't NEED a hot rod but a quick fun motor is fine

This is really a fun around town truck and light wheeling and fishing truck. Mostly for dirt roads in the back country, maybe some slick rock in Moab, but NOT building it for crawling.
I'd still hunt for a different engine. You could likely get one better suited to a Bronco and your plans, and even save a little money at the same time.
I hear you about the "don't need, but it might be cool" thing. But since this is a big expensive project and you'd like to enjoy it all the way around and not ever have to mess with it again (hopefully) it sounds to me like you should go for a better cam.
Nothing wrong with 330 hp actually. It's just where in the rpm range the torque peaks that makes the difference. If getting a better truck engine means losing 30 or 40 horsepower at the top though, I would not consider that a loss. After all, remember your '68 probably had the equivalent of 170 hp at the flywheel. I know it was rated at 200 if I remember, but that was the "gross" horsepower rating that changed to "net" after '71. So your 340hp is very likely literally DOUBLE the horsepower of your original 289.
Something to think about when wondering if it's enough. You can really wake up a Bronco with the right gearing and 250 actual hp. Three hundred's a big bonus.
Especially if it makes 350lbs of torque at 2000 rpm!
Paul