Valve cover gaskets-ignition coil failed

As far as the ignition coil and spark plugs, damage to them is probably not likely, but damaging the spark plug wire boots, (if they have never been done), is almost a given as they are hard and brittle from age. The fact that the plugs and coils need replacement are from ignition diagnostics being performed.
The first repair shop did not necessarily, I am not siding with anyone, try to do you wrong, but did what was asked of him and probably should have told you the other issues and not have delivered the vehicle without explaining what was going on.
This did not all happen over night, but the repair of the valve cover gasket probably caused the plug wires to essentially, "Not Connect" or transfer enough voltage to the spark plugs, which certainly need replacing if they never have, and with low voltage from a weak coil, can add up to the problems you are experiencing.
It sounds like the ignition system will be straightened out and you might ask about the condition of the fuel system and fuel management system.

The intake and throttle body could be dirty, as well as the O2 Sensor, Idle Air Control Valve, (IACV), and the Fast Idle Thermo, (FIT). If the Intake tract and throttle body are dirty, that can affect performance.
I hope this helps. We are always here if you have any other questions.

My first instinct is that the first shop was not very professional. When a vehicle is delivered to a customer, it should be test driven and any issues brought to attention before it is picked up. Before that happens, the car should be looked at and the service tech should take into consideration the mileage, last service done and the condition of anything he will be working around and the overall condition the car is in. A lot of people don't like it when a service tech suggests more repairs. It is selling more for the shop, but a dependable repair shop will suggest items that need to be serviced. If he had just asked when the last time the spark plug wires were replaced, a lot of this could have been avoided or you would have at least felt like you were not being blind sided like you do now. If the plug wires have never been replaced, that is a no-brainer. If they are going to get pulled, they are going to probably fail and while the plug wires are off anyway, it would only cost for the parts as this is, "Overlap Labor". Meaning that the plug wires had to be, "Removed and Replaced", (R&R), so there is no extra labor charged since they are going to be R&R'ed anyway.
So, I do agree that the first repair shop is somewhat un-professional and should have done things differently. It should not cause Check Engine Lights to come on. Switching coils should not do that and I am not sure why he did not suggest the service that you are getting done now. All I can figure is that he did not want to look bad for not telling you how much the vehicle really needed.
The $900.00 is not an unreasonable estimate considering the diagnostics the repair shop had to do. In fact it is about right for the services stated and the vehicle certainly needs them and you will be amazed at what replacing said items will do for the trucks performance. You will get better gas mileage as well. So, don't take it all as bad. The services needed to be done, you just went to a repair shop that did not tell you everything it really needed and at least tell you that things like the plug wires may get damaged. Other than the plug wires though, I have to take your side as saying something like, "maybe I wired it wrong. Or, I tried switching coils", does not sit well with me either. There is not anything I can think of that could get wired wrong just from doing valve covers. If there is, a good tech would certainly keep up with it.
So, I am sorry you are in this position and I hope that you can sort of see the good side of the situation you are in.
In the future, when picking a repair shop, although if things go well with this one, (keep using them as loyalty to any merchant is a give and take and is good for all), there are links on this site to help you find a reputable repair shop near you. Look at the condition of the shop, is it clean and reasonably tidy? Does the equipment look outdated and worn? Does the staff carry a professional attitude?
These are a few things to look for in a good repair facility, not a guarantee though.
Let me know how it turns out.

I am glad to hear the information helped but I am so sorry for your situation. Vehicles are a pain in the ***.
I do agree that the first mechanic as you described the situation. Seemed shady.

A burnt valve comes from a lean air fuel ratio condition in the cylinder. Either a injector failed on that cylinder or you had a intake manifold leak right next to the ort or an exhaust leak right nest to the port for that cylinder.

So, now am I to understand that all the aforementioned repairs are complete and the burnt valve is making the truck still perform badly or just as bad as when you brought it to the second repair facility?

A this pint I would recommend trying an On Board Diagnostic scan. If you have the repair shop that you are at now do it, it is simply hooking up a plug and reading failure codes stored in the trucks' computer. Ask to watch. I think I mentioned this to you before. I am so confused with 2 other customers, one of them has a Montero. Believe it or not, that I am loosing track sometimes.
The code reader will say right out if there is an issue. The display screen will say if there is something wrong. It still might not pick up the issue. So, ask which cylinder it is and if it has low compression form the burnt valve or how it is affecting the performance. Ask if he has an infrared thermometer and ask if he will point it at the exhaust manifold for the bad cylinder. It should be considerably cooler than the other cylinders as it is not firing. If that does not work, drop a few drops of water on a good cylinder and then the one in question as the good one should boil off the water more quickly that the failed one.

I will be unable to check post via computer for a bit. So if you can e mail me your response, I can replay to you more quickly using me cell phone.
My e mail is beck. Bradley333@hotmail. Com.
Let me now how things go and I will reply ASAP.