Replacing spark plugs

You can drain about a half gallon of coolant to a clean container so you can reuse it.

And the car is NOT running properly if it is only running on the battery.
You said after you connected the hose, it started running fine.
But only on the battery?

??????????????????????????????

 

Do not remove the intake manifold or the EGR system! You need to first get the engine running like it was running before you replaced the spark plugs. Working on a different part of the engine will only make things worse. You do not want to go down any more rabbit holes. You seemed to go down many rabbit holes with the Gen 2 that you previously owned.

 

If you don't know when the coolant was changed last, you might as well change it now. Drain coolant before removing EGR parts. But if you don't want to go that route, don't worry about losing too ouch coolant. May be a cup or two will come out of the hoses. Just refill the reservoir to the top line.

 

And a frenzy of belated and misguided “maintenance” ain’t helping matters. I was thinking to mention the “drain two quarts of coolant into clean container at the outset” ploy (alluded to by @ASRDogman ?), and mention the relevant links in my signature, but maybe it’ll just muddy the waters more.

OP’s most likely got a blown head gasket. It’d be best to slow down, check that first, preferably by a pro. Or just sell it, move on.

 

You cannot ignore the EGR cooler and the EGR valve. They are critical blockages in addition to the intake.

 

Are the holes completely blocked? If not, use a .22 cal gun bore brush and a drill.
With Gunk, the flammable one, not the foamy one, that is useless.
It cleans them out in seconds. If you aren't going to clean the cooler, don't waste your time
on the pipe. The EGR Cooler is what clogs.

Make sure you use the Toyota 50/50 coolant or you could turn whatever is in there to jell....
Drain it from the radiator. And you might as well drain the inverter coolant also.
Don't be fooled into believe anything else is "compatible", it really isn't.

When you refill the coolant, go very very slow, one or two cups at a time. You'll hear it trickle down.
And it will push the air out. If you go to fast, you'll trap the air.

 

I would just run a slim brush a bit, give it a squirt of brake cleaner, work it around with the brush. Don't use anything caustic, Oxi-Clean, oven cleaner, lye solution, they'll all react with the embedded metal bits in the intake manifold.

 

If you drain a couple of quarts of coolant (into a clean container) before disconnecting hoses to the EGR cooler, it's more or less dry, above the waterline. The only other coolant hoses involved are at the throttle body, and they don't actually need to be removed: the throttle body can be lifted off and cleaned right there, and/or tied to the inverter cables.

When everything's reassembled, just pour that drained coolant back into the reservoir, worked for me.

Check out the top 2 links in my signature, lots of EGR info. If you're on a phone turn it landscape to see signatures.

If you think EGR cleaning this late, is going to somehow stop the engine shakes, well what can I say. It's commendable, but you likely will be dealing with head gasket soon. My 2 cents, properly functioning EGR is crucial to head gasket wellness, and that requires cleaning at least every 50k miles.