Backed up all my stuff and scrubbed drive E:\.  Reinstalled FS9 from the four disks as E:\Flight Simulator 9 - nothing else on the drive - no addons, program files - nothing.   It's still very slow through the splashscreen and into the 'create a flight' window.  Don't always see the mini loading window on the splashscreen.  At the 'create a flight', settings' or any other windows, response to mouse or keyboard input is slower than molasses.  Actual flight seems almost normal - all default but OK.  Exit is once again super slow and just before you go to splashscreen, on exit, I get a 2D cockpit of the plane just flown with a solid red bar where the parking brakes banner is located on opening.  My graphics card (8800GTS) was fine before everything went TU but perhaps another driver (have the latest (191.7) would be better? 
Addendum:  Uninstalled from E: and installed on C: - no difference.  Noticed when I flew it a massive FPS of 5.5 to 6 so the graphics card's not doing much.  Changed drivers - no joy - back to the latest 191.7.  Was under the impression that you got a fresh .cfg when you reinstalled.  All my 'search' has revealed is my old modified .cfg so can't tell if the video card is included on the new install. 

It sounds as if you did not "clean up" after the un-install.

Only those items which were installed from the disks will be removed by the FS2004 un-install routine.

Many items are therefore "left over" - such as the FS9.cfg file which is not created until you run the sim the first time - and they must be manually deleted.

After an un-install search your HD very carefully (enable show hidden files and folders) and delete whatever was left behind that relates to FS2004.  That would include any saved flights, the Flight Simulator 9 folder, and the FS9 folder where the FS9.cfg (and other related files) are.

Usually found here:

C:\Documents and Settings\Your User Name\Application Data\Microsoft\FS9

Only then will you get a good clean install.

ShaneG wrote on Oct 27^th, 2009 at 7:09am:
But that's the irony.  All I have is a fresh install, brand new FS.cfg with no addons.  It's not so much overall slow, as in overloaded, it's very reluctant to repond to any mouse input selections (several tries, lots of lengthy black screens and plenty of patience) prior to flying then, when I hit 'shift Z', a measly 10 FPS when I was getting 75 prior to this problem.  I've yet to investigate Opa's suggestions so - "News at eleven"  .

Mr Shanks wrote on Oct 27^th, 2009 at 1:25pm:
Speaking of understatements  .  Other than FS9, my computer seems normal -everything functions well.  As far as unhealthy downloads, they all seem to be doing their thing but something is certainly amiss and corrupting FS9.  In the opening stages, paging from settings to create a flight - anything involving mouse inputs - deplorably slow to the point of black screens.  Reaching flight, the frame rates are single digit where before they were in the seventies - all sliders maxed.  I've done a fresh install on two separate drives and hopefully removed any debris from the previous install(s).  My gut instinct says the card isn't talking to the game, yet I've checked all I can think of and it says 'normal'.  Keeps me alert  .  Take care of my homeland - Edinburgh, 1938.

beaky wrote on Oct 28^th, 2009 at 9:03am:
That thing shows up everywhere, including the fs9.cfg, it's just 'not there' when I run the game  .  Did another complete uninstall, as per Microsoft Support.  Got rid of the fs9 folder, Flight Simulator files and removed any fs9 registry entries.  Will reinstall and keep my fingers crossed - stay tuned  .