Thank you for your question.
What you can do is to continue to be the best father you can. your child will soon see the truth and your relationship with your son will prosper. An 8 year old has concrete thought processes and he will grasp the truth of the situation in his own way.
You and your wife are not, from what you state, entered into the separation period for the same reason. As you stated, she things this is a time to let things cool off and to move to reconciliation; while for you this is a time to transition to divorce. You are wise to understand the miscommunication and how it affects what is going on.
Your wife is reluctant to allow another woman to have influence over the child, and she would feel the other woman is a threat to her chance to reconcile with you. This means she will, use the child visitation and joint custody arrangements to try to control you in a way to minimize contact with the other woman.
From a legal perspective, you can enforce the separation agreement. She is interfering with custody and visitation which is a crime in most states.
IN this case, for the good of your relationship with your son, you may have to hire an attorney to get a court order to enforce the separation agreement.
What your wife is doing is fostering conditions of Parental Alienation Syndrome: http://www.breakthroughparenting.com/PAS.htm
so at this point, you may also wish to bring in social work services to evaluate your child's family environment with his mother.
When you do get visitation started, my recommendation is to take it slow introducing your son to a new companion, unless this new companion is sure to be permanent and or very long term. The general shelf life of a non-committed relationship (where both parties are looking to marriage) is about 2 to 3 years. Children react differently toward divorce and separation. IN some instances they blame themselves for the parents breaking up. During a period of time, they may attempt to get mommy and daddy back together; but sometime along the line, most will express a need in some way for a replacement parent.
If you introduce your child to women you date, it is possible they can form early attachments to these women. In so doing, when it does not work out between you, the child is hurt once again. This is very emotionally damaging to the child. For this reason, I do not recommend early frequent dating, or allowing your child to meet these women.
If you are in a new relationship already, that looks like it is going long term, then introducing your child in a non-threatening way is the best option.
Ways that seem to work best are:
1. Meeting for the first time at a church pot-luck, etc.
2. Meeting at lunch.
3. Meeting at a park or zoo.
Let your son know that you would like him to meet a new friend. Then introduce her as your friend. If your son asks, make sure he knows this is not a replacement for mommy, that she is just a friend. More than that is not necessary for a 9 year old.
Over time, you will want to talk to your son about the relationship and have a talk where you let your son know of intend on marrying this woman (if the relationship reaches that point). It will be important to let the child know that this is not a replacement for his mother; that he still has his real mother. Your new woman needs to take it slow and not try to force herself into your son's life as a mother figure. That will occur over time.