Run the terminal.
Goto the directory which holds MacPhex.app.
Goto MacPhex.app/Contents/Resources/Java/
Copy all the new phex files into this directory.
cd ..
Make your MRJApp.properties look like this:
# This file is loaded by the Java Virtual Machine on MacOS.
# Most information herein is loaded into the JVM System properties upon launch.
# The '#' character denotes a comment that occupies the rest of the line.
# Each property should occupy a single line. For example:
#com.apple.mrj.application.classpath=MyApplication .jar
#com.apple.mrj.application.main=MyMainClass

com.apple.mrj.application.gc.async=true
com.apple.mrj.application.stderr=$SYSTEM
com.apple.mrj.application.classpath=Contents/Resources/Java/:Contents/Resources/Java/Phex050.jar
com.apple.mrj.application.stderr.append=false
com.apple.mrj.application.stdout.append=false
com.apple.macos.useScreenMenuBar=true
com.apple.mrj.application.stdin=/dev/null
com.apple.mrj.application.verify=remote
com.apple.mrj.application.classloading.verbose=fal se
com.apple.mrj.application.gc.min=2M
com.apple.mrj.application.stdout.unicode=false
com.apple.mrj.application.stderr.unicode=false
com.apple.mrj.application.gc.max=64M
com.apple.mrj.application.stdout=$SYSTEM
com.apple.mrj.application.stderr.file.creator=CWIE
com.apple.mrj.application.build.version=1.0
com.apple.mrj.application.main=StartPhex
com.apple.mrj.application.jitc.disable=false
com.apple.mrj.application.parameters=
com.apple.mrj.application.profiling=false
com.apple.mrj.application.stdout.file.creator=CWIE
com.apple.mrj.application.growbox.intrudes=true

This will let phex050 run under MacOS X 10.0.3.
I still haven't worked out how to get it to save the dowload list though.
It creates the phexdownload.xml file, but never populates it.
Next time if launches, it reads the new file instead of the old one. It also fails to update the old file