You should have done what was already recommended, and spent nothing to do it.
Loosen the intake bolts and move the whole intake manifold and carb up or down and it would line up fine.
Oh well.

 

Looks like your heads are machined from billet, which is consistent with their other products, however that shouldn't change the location of those mounting holes.

 

Just went thru exact same thing 3 days ago. Went to install S&S air cleaner on my Evo. Had been running a different air cleaner on my Super E. Back plate holes didn't line up, just like he first pictured.
Simply loosened the intake flange bolts and "rotated" the whole intake manifold until it lined up. Tightened everything up and it's perfect.
No need to buy anything and rig it.

 

Whenever I put on heads that have been machined (Decked) I always check the for the fit of the intake runner to the cylinder head ports and then have to hand fit the intake runner to the cylinder head ports. Usually done with a large flat file. Hand tooling... I do this because what's the sense of putting on good heads if the ports and runners don't match properly....

 

Even a completely stock motor can have the issue he had. The manifold can be rotated slightly, which will change the positon of the carb, which will affect the position of the back plate.
No brainer.
He went and spent money to buy different parts, then had to rig it up to try to make it work.

 

I appreciate all the criticisms from my fellow members. The S&S Stealth cleaner cost $120.00. I got my money back for it. The breather bolts and fittings cost $40.00. I already had the early backing plate. I did not "rig it up to try to make it work." I did it like I wanted and did away the breather return into the carb. I am satisfied with my "rig up". I am here. Everyone. I can hear you. Quit referring to me in the third person.

 

Not everyone criticized you and not everyone put you in the third person. Some will and some won't... It's all how you want to look at it .. take the good and hopefully it'll all work out for you... Glad you got it worked out... We're you able to support the carb with the 2 breather bolts.... If so who's kit did you use? Got a pick?

 

Glad you're happy.
For anyone else running into the same issue, just loosen the intake, realign, tighten, and be done.

 

pjb. That is all well and good. Just beware of a manifold leak. Especially if your o-rings are old and brittle. It might be a good idea to replace those o-rings since you "broke the seal" on them. I am lazy. That is one reason I did not move the manifold. It might be a blessing in disguise that the Stealth did not line up.
When all is said and done. At the end of the day. All that matters is I got what I wanted and I did it my self. As I have mentioned several times. This is my first Evo. I am learning from the dedicated Evo owners here. Thanks.

 

98hotrodfatboy. I am afraid you are just going to have to go back and read all the post and look at the pics. I have it all pretty much spelled out. As pjb said. I rigged it all up to try and to make it work.