I have the monsoon sound in my 99 TA and I want to replace my head unit and possibly speakers. Is there a harness that will bypass the monsoon amp so that I don't have to rewire the whole car for new speakers?

 

I don't think anybody selling it - just find a wiring diagram and bypass the amp yourself.
If you are going to use stock speakers for a while it is bad idea to bypass Monsoon - they are 2 ohm speakers and you can burn your aftermarket headunit. You can connect it to Monsoon, no problems, many people run it that way.
When you will be upgrading all your speakers, it will be a good time to step away from Monsoon. Keep in mind, that to get a good sound you need a component speakers in front, and for them built-in HU amplifier likely will not be enough.