My 04 boxster wont respond to keyless entry, soft top and rear trunk

Check the battery in your transponder.

where is the transponder?

The transponder is the keyless entry fob that I am assuming that your Boxster isn't responding to. Are we both on the same page?

i put in a new battery in the transponder. The soft top or key or the rear trunk stopped working at the same time. I thought maybe it had a common fuse (which I checked) or common area I should look at...

Dose the transponder activate ANY of the components that it is supposed to?

The car itself could have a dead battery.

I believe the key transponder in the 2004 Boxster needs to be paired to the car again after the battery completely discharges, my 2009 997 certainly did. Your owners manual will describe the pairing process.