I think his remote is working fine because he can control the ML/MCL converter and gets music via Masterlink.

The BeoSound 9000 needs to be set to A-Opt 1 according to the manual and it acknowlegdes it by blinking the red standby LED once.

If it's not acknowledging the sequence may still be wrong _or_ the IR receiver needs to be done as Beobuddy stated before.

Concerning the sledge touching the CD back: See this thread.

OK all.  I know it took me some time, but here is the answer.

For the Remote not controlling the Beosound 9000:
New IR Circuit Board installed - all good.

Full story:
I ordered a new IR circuit board from Kirk at the B&O shop in Kansas City, Kansas.  Great guy and great shop.  It cost $90 and, if you follow only the instructions needed to get to the board, is not a really difficult install.  Kirk told me I did not have to remove the faceplate (the aluminum that the CD'd sit in) just move it a few inches to the right then uninstall and install the IR circuit board. 

I ended up taking it all off because I was following written instructions instead of thinking.  Took much longer to reassemble; ended up with an extra part (I will ask you all) but I improvised and got it all going.

Sledge hitting CD or at least sounded like it:
The easy solution would have been to adjust the clamper with the two screws near the display.  I had to "revitalize" the flat springs then make the adjustment.  This was after trying many other things.  The two little allen head screws lift the outer edge of the clamper. 

So, now the problem:
Everything works.  But I took off the arm that attaches to the clamper (from the sledge under the display) and a little spring popped out.  It looks like the spring from a writing pen that your click.  I was hoping that was it, but no.  I found nothing in the area that would support that type of spring.  The service manual for the Mk 1 and Mk 3 do not show a spring in the area.  Its purpose is to keep the center of the clamper up when moving from CD to CD.  That was where I had to improvise.  I put some foam under the plastic cover that covers the arm. It had just enough force to push down the arm and raise center of the clamper.  Everything plays now.

Now the thanks:
Merry Christmas and Happy Holidays to all of you.  I appreciate the tips and thoughts.  Even if an answer does not solve my problem, it does help me keep thinking.  The IR sensor was one of my Christmas presents and I finished the project today.  A very happy moment for me.

Thanks all!