Well good news is I dont have to pull the plugs, It ended up being one of the coils which solved one issue. Running much better now pretty smooth at idle but It’s still pretty rough at higher speeds. About 40+ it still tends to vibrate unless you give it alot of gas which will smooth it out. Anyone know what might be causing that? I’m thinking transmission fluid is overfilled but unsure if that would even cause that…Also Unsure on anything else that might…
“Pretty smooth at idle” makes me think you may still have misfire or possibly a fuel related issue or (god forbid) a cylinder with low compression.
Do you have a scan tool? have you looked at your fuel trims? If not a visit to your local mechanic might be in order. Its usually just an hour labor to plug in the box and see how the engine is actually doing… and they can also do a “relative” compression test in about 5 min with just a amp clamp on the battery cable… If that all seems good then I would suspect a drive shaft imbalance issue or possibly a bad tire/ujoint/etc…
Hopefully you wont have to pull the spark plugs “if its a three valve head” cause nine times out of ten some if not all will break and its a real PITA to get the broken part out of the head…
If you do need to change plugs, get the engine nice and hot before you try to remove the plugs… sometimes that helps.
I presume you mean in D at 40 mph. Try driving it at 40 mph but in a lower gear, see if that has any effect. Another test, in N at 40 mph, coasting. My guesses are an engine/transmission mount problem, or a driveshaft-u-joint problem. If you have a two piece drive shaft, make sure it is about right in the middle of its fore-aft travel. If it bottoms out it can cause a vibration. If you have a center carrier bearing in the middle of the driveshaft, those are notorious here for causing vibrations if they are faulty or not properly adjusted.
Thanks everyone for the help 
Yes Drive at 40 I will check N tommorow and lower gears also and see what happens. I dont think it is a driveshaft issue, But I really wouldn’t know or how to tell. I know I marked them, and replaced them in the exact same orientation as I took them off.
Some versions of the f150 uses a center bearing to support the driveshaft. If you have that version, consider that a prime suspect. There’s a tsb for vibrations at highway speed caused by that part, TSB 07-10-9.
I’d have to disagree. Yes these 2 piece plugs suck but you should never remove plugs from a hot aluminum head. You are much more likely to damage the threads in the head which will lead to a more costly repair. I once removed a plug from a hot head and when the plug came out so did all the threads from the aluminum head.
Always use anti seize on the threads when reinstalling in aluminum head.
I recently changed the plugs on my 3v V10. The new motorcraft plugs are no longer the 2 piece design. From what I read ford resolved this issue sometime in 2008 production year.
Well I went ahead and checked a few more things, And tried 1 2 which drive smooth but dont really get up to highway speed. Shifting into N does stop the vibration, but the vibration is really only happening when you are accelerating at higher speeds. I also heard somewhere to try it with O/D off and low and behold the Vibrations stopped. Not really sure what that means though or what to do to fix it so it can be driven in O/D. If anyone has yet more advice or experience dealing with this.
I’m not sure what year your 3v triton V10 is
But I’ll say a few things . . .
If the engine originally came with the mile-long 2-piece plugs, you can’t just install the newer plugs . . . which are more conventional, but still pretty long . . . instead. The newer design also has different coils
Whatever the engine came with, you have to stick with the same design, either Ford or aftermarket, but you can’t just “upgrade” to a newer style ignition system
I’ve done plenty of ignition tune-ups on 2008 model year 3V Tritons which had the 2-piece plug design
2009 model year and up definitely have a plug with a more conventional electrode design
But for op’s 2006 Ford F-150 . . . they can’t just “upgrade”
So definite vibrations felt at 40+ mph, but no vibrations at the same speed in N coasting, and none w/overdrive off either. Good clues. At this point it could be related to engine loading or transmission/post-transmission loading. Since the only thing you replaced was the transmission, seems like a good bet the engine is ok, and the problem is either the transmission itself, or its interface at either end (w/the crankshaft, or with the driveshaft).
My guess would be the torque converter clutch, I hear this gives that issue. But really have no idea. I have seen a few things on transmission “Shudder” but still dont fully understand the root cause. Everything I see on it seems like they are just trying to sell the treatment to add into your fluid…
Also thought I might add, Power steering is pretty stiff also. Not sure if it would be related…