Upgrade ColdFusion 9 to 9.0.1

None of your changes are in effect. Hence ColdFusion 9 is still on the original version,  9,0,0,251028.

Luckily for you. Had the steps you had done gone through, you would have messed the server up.

You are on ColdFusion 9. Going from 9 to 9.0.1 is not a ColdFusion update, as you say. It is a ColdFusion upgrade. So the first thing you had to do was upgrade from ColdFusion 9 to ColdFusion 9.0.1.

You will find the ColdFusion 9.0.1 upgrade installer at the CFML Repo. Follow the links on the Google drive till you get to the 9.0.1 installer.

After you install 9.0.1, follow the steps in the link you mentioned above. In so doing, you will update CF9.0.1 with Hot Fix 4.

You mentioned another problem, with Java. That was most probably caused because you had been making the JVM changes in the wrong config file. The correct file is jvm.config, not config.jvm.

The following statement also sends a red flag:

"... Copied MSVCR100.dll from C:\program files\java\jdk1.7.0_21\jre\bin\ folder to CF9\runtime\bin. Changed the config.jvm to Java.home=C:/Program Files/Java/jdk1.7.0_80/." 

I would advise you not to mix libraries from 2 separate JDK versions. Choose one JDK version and stick with it.