I should know this answer, but for some reason it is not getting right in my mind.
To install the timing chains on my 1999 5.4. First I rotate the crank shaft so the dot on the gear is at the 6 o:clock position. Or straight down as you look at the engine from the front.
The crank shaft timing gear is the double gear, both left and right chain sprockets.
The dot on the crank gear is as stated at 6 o'clock. I then take the right? timing chain (the one on the rear gear) and place the single darker link ON the same tooth behind the tooth with the dot. Then place it on the cam gear so the line on that gear is between the 2 darker links.
Same proceedure for the other chain, except of course on the front sprocket. Single dark link on the tooth with the dot and double dark links so the cam line is between the 2 links.
Now, my confusion. Do I need to set #1 to TDC? Or does lining the crank gear at 6 o'clock and lining up the cam marks set everything where it needs to be in the cycles? I just can't get my mind on if it will be possible to be 180 degrees off by lining up the timing marks on the gears with the chain links.

 

Got the chains on with the proceedures found on here. Single darker link on the gear tooth with the dot on the crank gear, cam gear tooth with the line centered between the 2 darker links. The engine will turn with a wrench without any interferrance.
When I turn the engine with a wrench on the front bolt in the crankshaft, the cam will turn a little, meet resistance, then snap the rest of the way turning and make the chains jump a little. I am assuming this is because of the valve spring pressure on the cam? Is this normal?

 

Sounds like its in time, did you time it before you removed the chains and lock the passenger cam from spinning?

 

No, I didn't. Well, actually I did mark where the chains were on each sprocket when I started tearing the engine down, but the damage I found I tore down more than just the timing set. From my other posts, I had an issue with the timing chain guide breaking allowing the chains to rub on the cover. The oil pickup tube got clogged with metal filings. So, the cams came off. I had to re-time it from the beginning.

 

So I had to tear mine down to replace oil pump and chain guides so I decided to do it all. When I took the timing chains off I didn't pin the cams and they turned. Mistake one. So the next idiotic thing I did was turn the cams manually forward and crankshaft too. Now the passenger cam is at 2 o clock, the drivers cam at 3 o'clock and the crank key at 12 o clock. So the passenger cam won't turn back or keep rotating forward and the crank won't rotate forward either. Help!

 

If you get the crank in the right position (retarded a few degrees from TDC)
The cams should turn and allow to be lined up
Then you can advance the crank to TDC and be ready for the chains
Otherwise you can pull the cam caps up and allow the cam or cams to come up and get it lined up that way
Hold your mouth right
Good luck

 

I have one but never opened, just a pic in my mind. But IF you could, do 1 chain, the rear to my preference. Then the front. Maybe this is not possible. And new guides...!

 

No question is dumb
When you do as it tells you, (crank at 6 and you use the black links) (as you have done), that assures you that #1 was at TDC and the cams were lined up.
You should be good to go
Yes, replace the tensioners and guides with Ford parts
Consider replacing the oil pump

 

I've read that Melling has a v good oil pump that will deliver an important lil bit more oil... Not too costly.

 

That is the one I would use
A real pain to replace with the oil pan on but it can be done