There's a reason insurance companies write these off... they're cheaper to replace than to fix

https://www.youtube.com/watch?v=ljXqZ4Do6uQ

@mountainmanjoe is right.

The day this vehicle got submerged, was the moment when all bets about Toyota reliability & over-engineering went out the window.

That truck is now scrap. Don’t waste your time, energy & money trying to beat a dead horse. 

Get a full refund and look for one that isn’t salvaged/flooded.

It might not even worth fixing it. Realize that flood can damage all the electronics, the automatic transmission, the engine, ... you name it. Replacing the parts is the cheapest and safest way to do and they are not cheap either. The main issue is within electronics, water damage makes the computers go haywire and chasing the source os issues is almost impossible.  

And how are you going to deal with the salvaged title?  It's worthless except for parts or scrap metal.

Unfortunately it's very hard (actually impossible) to see a good outcome here.

Yeah your taking a BIG risk here. Unless you can spot what they would call "the HIGH water mark", all bets are off. Especially with all the electrical/computers.

I hope you didn’t put much money on that truck, but all bets are off when it comes to reliability and things going smoothly, as others have said.  Then again you said you bought a project truck - I wish you luck with that.  Ideally, I would say to plug in a full-system scan tool that can scan all systems on board to see what Faults/Codes are thrown - those won’t trigger CEL light necessarily.  But I would expect random electrical gremlins to pop up depending on what was damaged.  This is going to be some project alright;  hope it works out but going with a flooded project car was probably not a good idea.

I ended up buying a flood vehicle unknowingly.  The flywheel rusted to the clutch plate. Never, never, never again. They are money pits. The water causes internal damage.  The automatic transmission clutches turn to mush. You'll spend thousands.  

I think you get the idea from the above.  Hopefully you didn’t pay too much.  More hopefully you can get out of the deal.  I’m sympathetic; used trucks prices are all distorted right now, Tundra especially.  A lot of people are desperate.

That said, if you are stuck with it...

Drive it, and see what happens. Get a good scan tool and learn how to use it. Maybe you’ll get lucky.

I had a 2014 Tundra.  Even with all the bells and whistles on the 1794 package, it was a pretty simple truck.  Not real electronics-heavy.  That’s why it got 14mpg. The silver lining is that if any vehicle is gonna get flooded and be ok, you’ve got it. As long as the previous owner didn’t bend a rod in one of the hydrolocked cylinders, you might be ok for a while.  

And, yeah, if you can get your money back, do it. 

You wanted something reliable, so you bought a flooded vehicle? 

{black}:idontknow:

Flooded = Salvage. Salvage = Junk. 

If you can get out of it, get out of it. Otherwise, enjoy the expensive life lesson.

I own 2 tundras.  One year 2000 and a 2007. The first generation Tundra is the most reliable ever. I change the timing belt and water pump every 90k miles with a kit made by Aisin. Aisin makes the Toyota branded parts. I buy the kit with the aisin water pump, aisin timing belt, koyo roller bearings and hydraulic tensioner. My family still drives it daily for 22 years with 300k miles. I drive it state wide. The big issue is how these were maintained.  I would not buy one without shop records showing the timing belt water pump replacement. Or get the price down to afford it. Only use oem parts. Instead of buying a flood truck, buy a first generation Tundra. There are T100 trucks still going strong.  I towed a 32 foot travel trailer with mine after adding helper springs in the rear. It was not as powerful as the 2007 5.7 L, when towing. But did the job. Used trucks are hyper inflated right now. Dealers have zero used cars and near zero new cars. A first gen tundra is a very reliable truck.

Toyota's reliability and over engineering are pretty much out the window in this type of situation.

There are a lot of variables that are unknown.

Was it salt or fresh water?  How deeply was the truck submerged, and for how long?

If you wanted a long term daily driver, you are looking at pulling the entire vehicle apart and performing a full inspection.

I would start off by searching youtube for videos of other flooded cars being rebuilt.

How to restore a flooded car

https://www.youtube.com/watch?v=SMSQKhOGJCk