I have been accumulating parts for the upper intake removal and want to know what is recommended to take care of while off. My truck is running well but has a intermittent rough idle. I have done a crude smoke test and had a very slight leak at the throttle shaft and brake booster connection. My valve covers are leaking which is the main fix. But while its all apart I plan the below. Let me know if I am missing anything.

Valve cover gaskets
Intake manifold gasket (between upper and lower)
Throttle body heater gasket
Spark Plug wires. I have cheap Napa wires and will replace with Kingsborne 8mm
Coils? Is it worth replacing while apart if you don't have any coil related codes or issues? Other than a rough idle. I figure if I replace I start with fresh coils and then have spares.
Injector seals. Maybe?
PVC - Done
Anything else?

I don't plan to get into the valley gasket.

 

I'm in the middle of putting my engine back together after basically doing this (and the valley pan gasket). Went one further by sending my injectors out for cleaning, too.

You"ll want to replace the o-ring for the heater coolant pipe that connects to the lower intake manifold, since it needs to be pulled to get the passenger-side valve cover off. Replace the rubber heater hoses and other coolant hoses if they seem original or old. No need to replace the ignition coils if you didn't have any issues, but if you're a bit of a completionist then RockAuto has the best price for brand new Bosch coil packs. Do the Extinct inline thermostat mod, maybe even grab the Carr4x4 aluminum lower coolant y-pipe while you're at it.

 

A set of refurbished Mustang 4-hole 19#/hr injectors probably come with the o-rings. Then you'll have a spare set of injectors to go along with your spare coils

 

What is this? Mustang injectors? Tell me more. Where would I find them?

 

Do the PCV mod while you have things disassembled. Cheap and simple, and helps reduce oil seepage especially from the rocker cover gaskets.
Speaking of which -- you'll need a 1/4" drive, 12-point socket (I believe 8mm) for the rocker cover bolts. You might be able to get away with a deep socket if it's 3/8" drive.

 

I did the same as you last year and totally redid a top end rebuild of my Thor engine. Definitely take your time doing the job.
Valve cover gaskets - FEL-PRO gaskets FTW!!!
Intake manifold gasket (between upper and lower) - FEL-PRO gasket FTW!!!
Throttle body heater gasket - Don't bother. Read below.
Spark Plug wires. I have cheap Napa wires and will replace with Kingsborne 8mm - Changed mine to 10mm Taylor 409 HT Leads from a Mustang (I have to brag!). I had to build my own by cutting to length and crimp on the M4 terminal for the coil pack.
Coils? Is it worth replacing while apart if you don't have any coil related codes or issues? Other than a rough idle. I figure if I replace I start with fresh coils and then have spares. - I replace both sets of mine since I was going in there and I didn't know if the previous owner ever changed them.
Injector seals. Maybe? - I replace all 8 of my injectors and I'm glad I did.
PVC - Done - Right on!

IMHO... circumvent the throttle body heater. Run a 3/8" ID or 5/16" ID coolant hose (it's been awhile so it's of of the 2 measurements) from the top of the engine (where the hose to the TBH goes) and run it straight to the coolant reservoir bottle with some clamps.
No more leaking TBH because it's not being used.

 

I bought a set of used Mustang (Bosch) injectors for cheap and they have worked well for the past 3 years. Looked through my papers, but didn't find the purchase details. Looked on ebay and there are good ones in the $150 to $200 price range (set of 8) I would buy. Be sure to get original Bosch from a good seller. I would stay away from the cheap knock offs.

 

Thanks. I will check it out. I did read some are different lengths than others I need to try and sort that.

 

Or, just plug the lines going to and from the throttle body heater. The only purpose of that coolant circuit is to supply the TBH.

In my truck, I removed the nylon line running from the TBH to the reservoir and plugged the short hose on the small nipple on the reservoir. I've thus far left the hose that runs from the intake to the TBH in place but just plugged the end where it connected to the TBH. All is well.
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i can tell you what i did with my D1 - this does leave off a few items specific to the D2

clean the idle control valve
clean the maf
clean the intake plenums
clean the intake manifold
replace valley pan gasket
clean valve covers
replace valve cover gaskets
replace both valve cover breather hoses
check vacuum hoses
check fuel line hoses
clean rocker arms
clean push rods
replace lifters