Ok, I'll try again, thanks for not giving up on me guys, this is the last obstacle I foresee but it's a very problematic one...
 
Consider that a channel has inputs and outputs (lists). Those lists are different between the old and new system. And Sonar is not relying on the name aspect in order to make the correct associations on the new system. Rather Sonar is selecting things based on ordinal (best I can tell).  So if the 1st item in an input list was selected on the old system the same will be true on the new system - even though the 1st item might be a different device than before (with the desired device now residing in the 2nd location).  So when I open a project I now have to go down every channel's input & output list and correct things to point Sonar at the proper entry.   It doesn't matter whether it is an physical device or synth, MIDI or Audio, the same paradigm applies. 
 
BTW, I have no problem with plug-ins, everything is identical between old and new system as far as that goes, so no issues there.  It's just the channel I/O device/synth lists that are all futzed up.

Okay I understand now, I will 1st caution you just in case it had not occurred to you before you get moving along is if you start changing things to make them work, these new projects will not work once you get things back to normal(assuming we can).
 
As I stated mine are not alphabetized so strongly urge you to see if you can delete something from the middle of the alphabet and reinstall it to see where it lies in the list.  
 
I know we would like to think Sonar is smart enough to save the name of an I/O just in case things have to get moved around, but I suspect as you stated Sonar only uses the order of the devices to determine position.  This should be a ubiquitous topic if it posed the problem that you are describing every time someone changes hardware.  
 
I'll wait to see about the uninstall reinstall to change order of list to see if this solves the problem.

I spent easily 100 hours building this DAW and everything is working well, so I'm not keen on uninstalling things for a test.  Every time that sort of thing transpires something almost always gets borked up in the system..... residue left in the registry, other unknown consequences, etc.  
 
This I/O re-mapping dilemma has got to be a well-known problem, I just don't know what terms to search on....

if you use usb, have you seen this thread
http://forum.cakewalk.com/Sonar-X3-saving-MIDI-channels-problem-m3027710.aspx
 

Thanks for that info.  But nope, no USB in the picture.  The interfaces (both audio and MIDI) at the moment are are using PCI/PCIe Firewire.
 
But similar results as to what that thread stated...things getting all out of whack, but in my case the new layout is static.  Which is why I was inquiring as to how to force a change of order (other than possibly re-installing).  Surely this issue must have surfaced many times in the past.....I'm really perplexed I can't find anything about it so far.....
 
Here's a more specific example:  Assume an RME FF400 interface on both old and new system being used only for audio. And, on the old system the MIDI I/O was handled by an SBLive card (no audio).  Whereas the SBLive card is now gone on the new system in place of enabling the MIDI I/O on the RME FF400.  So basically there is a common audio interface between old and new system, but the MIDI aspects have changed.  This is now causing an ordering issue on the channel I/O selection.  Also, if I'm not mistaken, the fact I added a 2nd drum synth instrument to the new system seems to have further caused issues in the channel I/O selection lists.
 
 

I just found this.  Sounds like the same issue (at least as far as the MIDI aspects go).  However, nobody ever responded....
 
http://forum.cakewalk.com...?high=midi+input+order
 
Then, I found this, where there seems to be a debate over whether or not the ttsiq.ini file can be made to resolve MIDI and audio I/O mappings or not....
 
http://forum.cakewalk.com/Preferences-Devices-MIDI-Move-Checked-Devices-to-Top-m3368756.aspx?high=midi+input+order
 
Sonic

Ok, I'm going start another thread about a very specific aspect of this matter as this thread's topic is rather broad and getting a bit convoluted (mostly my own fault).
 
Right now it seems the main obstacle I face is the MIDI output list.  I'm going from previously having a MIDI out (the SBLive) to no MIDI out.  This throws the channel output list on the new system all out of whack and totally hoses up the ability of opening previous projects with a lot of manually tweaking every track.   I either need to select (add) a new MIDI input or find some way to stub a MIDI input at the top of the list so everything else previously below that in the list stays in proper order.
 
New thread on this more specific issue: http://forum.cakewalk.com...-m3673504.aspx#3673504