RADIO-----2 TRANSISTOR AMP-----SWR METER------ ANTENNA

Ok, when I check the SWR on my antenna it shows 1.1. When I turn the
amp on it shows over 3.x SWR. The antenna is rated at 5 KW. The amp
only puts out about 100 watts.

When I had this it was caused by arcing at the antenna. VSWR perfect with
low power, but it even made an audible noise when you screwed the power up.

1 - Try this using a band-pass filter:
RADIO--2 TRANSISTOR AMP--SWR METER--FILTER--DUMMY
If amp churns out **** then the filter will reflect it. If VSWR is good,
then:

2 - Eliminate your feeder (could be breaking down):
RADIO--2 TRANSISTOR AMP--SWR METER--FEEDER--DUMMY
When you do this you may even see a duff contact/joint.
If the feeder insulation is breaking down then VSWR rises again. If not
then:

3 - Check out the antenna / balun / feed points for strands of wire, smoke,
etc.