Did I miss something. I changed the rear value cover plus cleaned EGR tube, now but manifold and EGR tube does not align to it??

there is about a 2 inch space in between? is there a gasket?

I've replaced both of these. I'm having difficulty understanding what is going on. Do you have a better description? A picture,.?

I remember doing this job and this happening. I believe that I bolted the tube upside down once and it would not align, then I flipped it and it fit. Perhaps that's also your issue.

As I recall, it's quite easy to tighten the lower guide tube flange at the incorrect position, thereby creating the gap you're talking about in the upper flange.

Very loosely attach all of your mounting nuts.

With everything loose, position/mate the upper flange as necessary (don't forget the gasket and nut spacers) ... tighten the upper flange.

Then tighten the lower flange and you should be good to go.

This was it. I loosen the bottom bolts and align them all and it worked.