Thanks,
my pleasure to give something back after getting so much.
Here is a copy of how I set up .jwmrc to include the .jwmrc-mjwm file with the generated menu and run mjwm with the refresh command.
<?xml version="1.0"?>
<JWM>
<!-- The root menu. -->
<RootMenu onroot="12">
<Program icon="mini.xterm_32x32.xpm" label="Terminal">xterm</Program>
<Program label="File Manager">spacefm</Program>
<Separator/>
<Menu label="Favorites">
<Program label="Trelby">/opt/trelby/src/trelby.py</Program>
</Menu>
<Separator/>
<Include>$HOME/.jwmrc-mjwm</Include>
<Separator/>
<Menu label="Exit">
<Exit label="Logout" confirm="true" icon="quit.png"/>
<Program label="Reboot">gksu reboot</Program>
<Program label="Turn off">gksu halt</Program>
</Menu>
<Program label="Refresh Menu">mjwm; jwm -reload </Program>
<Restart label="Restart JWM" icon="restart.png"/>
</RootMenu>
<StartupCommand>nm-applet</StartupCommand>
<!-- Additional tray attributes: autohide, width, border, layer, layout -->
<Tray x="0" y="-1" height="32" autohide="false">
<!-- Additional TrayButton attribute: label -->
<TrayButton label="JWM">root:1</TrayButton>
<TrayButton label="_">showdesktop</TrayButton>
<!-- Additional Pager attribute: labeled -->
<Pager labeled="true"/>
<TaskList maxwidth="256"/>
<Dock/>
<!-- Additional Swallow attribute: height -->
<Swallow name="xload" width="64">
xload -nolabel -bg black -fg red -hl white
</Swallow>
<Clock format="%H:%M">xclock</Clock>
</Tray>
<!-- Visual Styles -->
<WindowStyle>
<Font>Sans-9:bold</Font>
<Width>4</Width>
<Height>21</Height>
<Corner>4</Corner>
<Foreground>#FFFFFF</Foreground>
<Background>#333333</Background>
<Outline>#000000</Outline>
<Opacity>0.5:0.9:0.1</Opacity>
<Active>
<Foreground>#FFFFFF</Foreground>
<Background>#333333</Background>
<Outline>#000000</Outline>
<Opacity>1.0</Opacity>
</Active>
</WindowStyle>
<TaskListStyle>
<Font>-*-fixed-*-r-*-*-10-*-*-*-*-*-*-*</Font>
<ActiveForeground>black</ActiveForeground>
<ActiveBackground>gray80:gray90</ActiveBackground>
<Foreground>black</Foreground>
<Background>gray90:gray80</Background>
</TaskListStyle>
<!-- Additional TrayStyle attribute: insert -->
<TrayStyle>
<Font>-*-fixed-*-r-*-*-10-*-*-*-*-*-*-*</Font>
<Background>gray20</Background>
<Foreground>Gray90</Foreground>
<Opacity>0.75</Opacity>
</TrayStyle>
<PagerStyle>
<Outline>black</Outline>
<Foreground>gray90</Foreground>
<Background>gray20</Background>
<ActiveForeground>#70849d</ActiveForeground>
<ActiveBackground>#2e3a67</ActiveBackground>
</PagerStyle>
<MenuStyle>
<Font>-*-fixed-*-r-*-*-10-*-*-*-*-*-*-*</Font>
<Foreground>gray90</Foreground>
<Background>gray20</Background>
<ActiveForeground>white</ActiveForeground>
<ActiveBackground>#70849d:#2e3a67</ActiveBackground>
<Opacity>0.85</Opacity>
</MenuStyle>
<PopupStyle>
<Font>-*-fixed-*-r-*-*-10-*-*-*-*-*-*-*</Font>
<Outline>black</Outline>
<Foreground>black</Foreground>
<Background>yellow</Background>
</PopupStyle>
<IconPath>
/usr/share/icons/wm-icons/32x32-gant
</IconPath>
<!-- Virtual Desktops -->
<!-- Desktop tags can be contained within Desktops for desktop names. -->
<Desktops width="4" height="2">
<!-- Default background. Note that a Background tag can be
contained within a Desktop tag to give a specific background
for that desktop.
-->
<Background type="image">/usr/share/wallpapers/jwm.png</Background>
</Desktops>
<!-- Double click speed (in milliseconds) -->
<DoubleClickSpeed>400</DoubleClickSpeed>
<!-- Double click delta (in pixels) -->
<DoubleClickDelta>2</DoubleClickDelta>
<!-- The focus model (sloppy or click) -->
<FocusModel>sloppy</FocusModel>
<!-- The snap mode (none, screen, or border) -->
<SnapMode distance="10">border</SnapMode>
<!-- The move mode (outline or opaque) -->
<MoveMode>opaque</MoveMode>
<!-- The resize mode (outline or opaque) -->
<ResizeMode>opaque</ResizeMode>
<StartupCommand>gkrellm</StartupCommand>
<StartupCommand>sleep 2s && conky -c ~/.conky/conkyrc_all &</StartupCommand>
<StartupCommand>sleep 2s && conky -c ~/.conky/conkyrc_key &</StartupCommand>
<!-- Key bindings -->
<Key key="Up">up</Key>
<Key key="Down">down</Key>
<Key key="Right">right</Key>
<Key key="Left">left</Key>
<Key key="h">left</Key>
<Key key="j">down</Key>
<Key key="k">up</Key>
<Key key="l">right</Key>
<Key key="Return">select</Key>
<Key key="Escape">escape</Key>
<Key mask="A" key="Tab">next</Key>
<Key mask="A" key="F4">close</Key>
<Key mask="A" key="#">desktop#</Key>
<Key mask="A" key="F1">root:1</Key>
<Key mask="A" key="F2">window</Key>
<Key mask="A" key="F10">maximize</Key>
<Key mask="A" key="Right">rdesktop</Key>
<Key mask="A" key="Left">ldesktop</Key>
<Key mask="A" key="Up">udesktop</Key>
<Key mask="A" key="Down">ddesktop</Key>
</JWM>