Missing Midi Ports Sonar

Hey Wadrum.
You can re-order the midi outputs in Sonar under preferences > midi devices, then selecting or deselecing devices and clicking 'moved checked devices to top'. If it is simply a case of your midi outputs being re-ordered this will fix it.
 
However,  if I have understood your post correctly your problem may be a little more complex - the actual midi device name has changed due to being plugged into a different usb port? So the midisport is showing up in Sonars device list in the correct position, but with a different additional number next to it.
In this case the problem you are encountering is a windows issue regarding midi address assignment. If you plug some previously installed usb midi hardware into a different usb port,  windows will recognise it as a new device and add a driver instance accordingly. As far as I know there are only 2 solutions.  You can either reassign all of your mdi tracks to the new midi port number and resave your projects, or you can uninstall the midisport driver completely from windows,  then reinstall it. To do this, WITH THE MIDISPORT PLUGGED IN, go to control panel >device manager, find your midisport  under 'sound, video and game controllers', right click on it and select uninstall.  Then unplug the midi-sport and restart windows.  Now plug the midisport back in and follow the dialogue prompts to reinstall your driver.
 
This should return the midi-sport to position 0, so that it will show up in Sonar without any additional number. From that point on any time you restart windows and plug the midi sport into a different port, windows will see it as a new device and the number next to the driver will increase by one. If you continue to plug it into the same port, it will stay the same.

Hey Wadrum. Is there an uninstall option under control panel>programs for your midi interface software? If there is, try running that after you remove the midisport from control panel>device manager. 
 
You really want the interface to show up in 'position 0' (no additional number) as that is where it would go on any new installation. If it is there now I would stick with that port.
 
By reassigning the mdi tracks I mean within sonar, using the dropdown output menu on each midi track (don't use the dialogue that pops upon opening the project saying you have unassigned midi ports. The settings made there never stick).
 
If you use control + select to highlght all of the tracks you wish to reassign then press the control key and change one output drop down to the correct midi output, all selected tracks will change to the same output. If you then save the project this setting is stored.
If you have recorded using different port drivers you will have to do this at some stage for all of the projects to work consistently. Just make sure you keep your interface in the same USB port whenever you use it once done.