I pulled the car into the garage this morning. First thing I noticed was the coolant level was low.
. So I’m thinking now since I don’t see any antifreeze under the hood, I’m betting either the gasket between the water and the intake runner of No 1 cylinder is leaking ... What’s your thoughts?
That sounds the most logical at this point. Antifreeze disappearing without a puddle under the car isn't a good thing. My '05 5.4 has always had drips from the exhaust pipe that caused me concern, but in years it has never lost any coolant - so I just chocked it up to condensation.
You don't say, but which Dorman intake does your motor take? 615268 or 615278 or something else?
You say it ran fine for the first mile or so and then started the chuga-chuga or entered a limp mode. That suggests something moved or changed upsetting the ability to fire all cylinders. The "misfire on cylinder one", obviously points to cylinder one, but generally loss of one cylinder doesn't make the car undriveable. Sure you will be down 1/8 of the power and have a rougher idle, but absent some commanded limp mode, the car should still run and drive.
When you pulled the No. 1 plug, if it wasn't wet and when you turned the engine over with the plug out, there wasn't visible moisture being expelled - that's good. You risk hydraulic-lock if you have too much water leaking into a cylinder (and it doesn't take much). Water is incompressible, and any significant leakage into a cylinder will, on the compression stroke, risk bending a rod.
Do you have any measure of the amount of coolant that was lost (or that you are losing)? When you drained the coolant to do the manifold swap, it's not uncommon to fill the reservoir to the indicated level, start and have it run up to temp, only to find the next morning you need to add another half-quart or so as all air in the system is displaced and fluid is pulled from the reservoir on the fender. I know I had to do that after draining the radiator to remove the upper radiator and heater hose connections to do timing chains and cam phasers.
The other possibility is the gasket on the intake runner failed and you are drawing air directly into the cylinder. (that's why I asked which manifold you have). Looking at the Dorman models, the 615278 seems to have individual gaskets around each runner and the water ports, while the 615268 seems to have one gasket for each bank that would be fitted into a groove on the manifold (which at least appears to have more possibility of shifting on install).
You sound like you are taking all the steps necessary to isolate what is going on. There is no silver bullet. The only other thing you might want to do if you have a code reader that supports "live data" is to hook the analyzer up and look at the what the O2 sensors are reading. If you are leaking air on one bank, you would expect to see that bank reading significantly different from the other.
These are all just spitballed ideas that came to mind reading the post, sorry I've got nothing specific for you. Keep us posted on the progress.
