You got the ends right....NO gasket just RTV in a thick layer so, when you set the manifold it will kinda squish down and make a good seal. (no scoot'in the intake around, set it straight down in position!) I like to make up some alignment studs so when you set the mani down they will guide the mani in perfect position! A thin layer of RTV to hold the gaskets in place is needed. The alignment studs work great for this too.
I LIKE to also put a thin layer of RTV between the gaskets and the mani too. To make up for any irregularities that might be in the mani(although that's the job of the gasket, I guess) IMPORTANT to set the mani straight down no wiggling. Extra sealant around water openings can't hurt if not over-done.
Next...remove the alignment studs and replace with bolts and torque to specs. THEN....leave it alone to give the RTV time to set up.
Its gonna be sealed so.....when removing the mani next time, well its gonna be stuck.
Butt......that's what we want a "stuck down-water tight-air tight-seal!
Welcome to the forum!...Where you from??!!!
6sally6

1. I don't think any of the intake bolts go into the water jacket, but they are exposed to oil in the lifter valley.  It doesn't hurt to put a little sealant on them.  I like Form-A-Gasket #3 from Permatex for this as it never fully hardens. 

2. If you stick the gaskets on with gasket cement, or use a skin of silicone around the water passages (I recommend both, and some #3 around the ports doesn't hurt anything either) they must be compressed or they won't seal right, but you also want the gaskets held in the right position while installing the intake.  I apply my sealers to the head side only.  I make 4 studs (bolts with the heads cut off about 2-1/2" long) to lower the intake down evenly, then remove them, install the bolts, and torque to spec.  Let it dry over night.  Then the next day, remove it and make sure the gaskets are in the right spot.  This way you can fix them if they shifted.  If they're good I skin the water ports on the intake side with silicone and lay down 3/8" tall beads of silicone instead of the end gaskets and reinstall the intake the same way (using the guide studs), and torque it to spec.  Then retorque after the first heat cycle and keep an eye on it for the first couple times you run the car.  It seems like overkill, but Fords are very susceptible to the gaskets shifting and developing an oil leak between the valley and cylinders resulting in some hard to pinpoint running issues at idle. 

3. Let that RTV skin before setting the intake.

4. If the gaskets match the ports and water passages in your heads they are right.  You'll know if they don't.  The wrong ones are quite obviously wrong, particularly with the water passages. 

Thanks for the replies. I do have some alignment bolts that I use. Also I use my cherry-picker to lower that heavy iron manifold in place to avoid bumping or displacing the gaskets. The MS90116 gasket is what I used the first time and it was the one that leaked at the aft driver side head where that L-shaped channel goes around the water cutout. The end of that channel comes out past the intake and that's where it was dripping from. So I guess I may have not had enough Ultra Black RTV on the gasket in that area, yet had no leaks anywhere else. I'll try the install this weekend again.

6sally6 wrote:

SUHHHHHHHHHWHEEEEEEEEEEEEET ride!!!!!!
Hope you can bring it to the Bash-at-the-Beach this April 23-24-25th in  Myrtle Beach!
WOW!!!!!....69 IMHO is when Ford finally got-it-right!!
6sally6

Could not agree more. We need more than one 69 at the Bash.

Where do you call home Dreamer?
 

Quick trip from Atlanta to Columbia SC......then over to the coast. I've made it several times in my 66.....to visit family, on the way to Tulsa/Houston/Dallas/ and other places.
REALLY would like to get "an-eye-full" of that 69!!!
6sally6

I'll-keep-my-fangerz-crossed (as they say in Georgia)
I used the blue RTV because ...............its Ford blue colored.
6sally6
Bash 'invite' is still open!           Don't gotta drive a Mustang, ya know!