Can a verdict or criminal evidence from a civil trial effect or be used as evidence in a criminal trial relating to that issue?

Evidence, yes. Outcome, no.

What is considered a "final judgement" in a legal separation?

Merely file an amendment to the petition requesting a final judgement.

On May 2,2009 the court entered an Order (Doc.#5) directing the Government to show cause on or before September 4,2010(criminal)

Sounds like dismissal for failure to prosecute BUT we do do not know what the original charge was.

I got a called a really bad name at work, but nobody witnessed it and it was very offensive.

Sure you can complain. Then get over it.

Is my current income subject to alimony if I have I had a legal separation filed and orders were set in 2007.

Please see previous responses.

Can my felonies ever be brought down to misdemeanors? If so, what is the process?

Once you have satisfied ALL conditions of probation, 17(b) is tenable as may be 1203.4. Discuss specifics with counsel.

No. Perhaps a cert. of rehab or even remotely possible, a pardon. Seek counsel to discuss specifics.

Ex wife wants to get uncontested MSA changed by claiming duress or depression.

Hold your ground. She will just come back for more.

Is it considered adultery if you've been living apart for 2 months but not separated or divorced

As far as you are concerned, no such animal exists. Talk to an attorney in the IE.

Probably not, but they may try. Talk to counsel.