Timmy has a video where he installs a transmission temp gauge in a 98' and mounts the gauge in a little plastic housing thing that attaches to the driver side A-pillar. Looked pretty clean from what I remember, you should watch that video and see if that location would work for your needs.
Did you screw the amp directly to the metal below the carpet? I just installed a powered subwoofer under the driver seat of my 98 and it sounds great but does rattle a little bit. I'm trying to decide if it's a bad idea or not to screw the thing down directly into the sheet metal of the floor.
It is possible that part of the toothed plastic of the antenna mast that engages with and coils around the gear inside the power antenna motor broke off in there, preventing the new mast from retracting fully. If you get behind the passenger side fender liner you will see the motor wrapped in...