So I cranked up the power to the max setting on channels 20 and 40 and noticed that I could get to the cal setting to tune on the SWR Meter, but when I switched to see the SWR reading I would get 3.+ Now is that because it's feeding it too much power now?
try checking swr with the radios power set to midway, if it cures the 3.0:1 swr setting, chances are when you switched to full power on the front control knob, the radio has been internally set up for too much power and is spewing harmonics, which could be the reason for your highish swr reading, if this is the case then adjusting the radios internal AM/FM carrier settings lower may tame it.
the front control knob varies the carrier power between zero or thereabouts and whatever the internal preset is set to on maximum.if the internal preset is set to high then inevitably when you turn the external control to full power you will inevitably come across problems relating to the carrier level being set to high.
incidentally this is the same reason fitting an ext power control should NOT be done simply by replacing the internal preset with an external control, because when you open it full up you have nothing left inside to set the max limit the transistor can cope with before it spews harmonics,self oscillates or even worse burns up.
it can easily be done by leaving the preset intact and fitting a variable before the preset,its also a good idea to leave some resistance permanantly in line on top of the new variables resistance,like its done on many ranger/galaxy/connex radios.
cutting an antenna is a LAST resort, you can't replace what you've cut off, so its much better to be sure all your connections,cable and other equipment are up to scratch first, which incidentally is the cause of 95% or more of all antenna problems.