I recently purchased recording software. When I plug my guitar amp into the mic input jack it still records using the built in mic. I had the OS changed a few months ago. When I pull up the "Manage Audio Devices" window it only shows the internal mic. Is it likely not everything was installed properly when the OS was changed? Or something else?

You need to reinstall the sound and other multimedia devices.
The drivers are normally available from the manufactures web site.