Yes, the computer analogy is pretty good, but the proteins can be for signaling, enzymes, or other purposes..

Can the old co-exist with the new? Thats a question i have no idea about (I will be honest)

There are a few reasons why viruses from other species can't infect human cells (or well) generally it's a matter of the virus gaining entry to the cell to hijack cellular machinery (i will admit, it's been a few years since my virology courses) so physically differences at this stage generally prevents entry.

Interestingly there is a line of thought that some poorly adapted viruses can be oncogenic (causing cancers)

To everyone with more knowledge on this, please correct and accept my apologies if I butchered anything!