I am too doing this soon....have many questions as well, but this is what i have gathered so far....maybe someone can chime in and fill in the gaps.

level the boat to zero. (via the stringers or bottom...or both )

then set the intake at 4 degrees via where the suction housing bolts onto the intake. Also make sure its zero from side to side in relation to the stringers.

as far as the process of applying the epoxy putty....i dont know. do you set the intake then pack in the putty? or do you cake on the putty then set/level the intake?

i was thinking of putting jacks under the boat holding the intake up and using the bolts to level it out then using putty to seal it up.

4 degress? meaning the rear is higher than the front?

yes.

you will notice that the intake has 4 degrees in it. setting the top part 4 degrees will set the base of the intake into the boat at zero.

Not if you're measuring your angle on the suction housing flange.

isnt it the suction housing flange that you want to have 4 degrees....right?

yes, this is where the angle needs to be measured from, the intake is all one piece so if the flange is good, then the intake is good.

ok, so then his comment is correct saying its 4 degrees with the rear higher then the front 

he is basically saying the rear part of the flange should be higher then the front of the flange. (ex not -4 degrees)  ...not the entire intake.  

im confused too. and dont know what im talking about. its my first day back to reality after a great 4 day weekend. my mind is scrambled. pay no attention to me.

SO to get the intake level with the hull bottom I need to have 4 deg on the jet mounting flange this will put the rear of the jet flange  lower than the front of the flange

BINGO!

I would get the epoxy area as clean as you can get it. Use some mineral spirits or denatured alcohol to clean it after you've got it roughed/sanded. I wouldn't paint the area the intake sits in, it will be covered with epoxy once the intake is set anyway so you won't see it. As for the intake, I'd rough sand the epoxy area, paint what you'll see once it's set. Mix up your epoxy, put some on the intake and some on the hull area. Set the intake, get it leveled and squared up and set some dead weight on it to keep it from moving on you. Not so much weight that it affects your set. You can tape off the hull so once the epoxy dries you can pull the tape and have a nice finished line, same thing on the bottom and on the intake itself.

I know this sounds obvious but also make sure the centerline of the itake is aimed right down the center of the keel. I've actually seen pumps mounted pointing left or right of center. Draw a line on the intake right down the center and then run a snap line from the keel center in the bow to the transom directly above the keel.  While you are getting all your angles right be sure to check that the line is directly over and straight with the snap line.