Try unpligging AND removing the faderport in control surface settings.  I find it can be terribly problematic, particularly if you load a project that used different audio/midi outs to your current setup.

I can't tell how many devices are connected directly to SONAR (i.e. defined in preferences as devices) from the .sig but my first inclination would be to see how fast it boots with just the MOTU connected.

There  is something wrong if the app takes that long to startup. I takes about 3-5 seconds for X3 to launch on my machine which is a core I7 950 with only 6GB. I also have a MOTU firewire interface and am running Windows 8.1. 2 minutes is drastically slow.
 
Also what do you mean when you say plugin manager takes long to load - which plugin manager? The one from the tools menu or did you mean the plugin Browser. 
Any antivirus or background file scanning software or utilities can drastically slow down application load times especially VST scanning since they check every dll being loaded agains their database - online sometimes!
Also some AV software doesn't really fully disable even when you turn it off. I suggest never running 3rd party AV on a DAW except for Microsoft's security essentials.
Do you have development tools or other utilieties on the machine that can impact this?
 
If you have already tried the suggestions in this thread and they don't work please call support and they can work through troubleshooting various things with you. 
 

gustabo
CakeAlexS, when you say try unplugging my devices, do you mean faderport, my keyboard controller?
My MOTU has the latest drivers installed, Windows Update is current, and as mentioned, plugin scan is set to manual.
I'll try the DriverBoost...

Any device apart from keyboard/mouse/monitor. Hubs as well.. See what happens and rule them out. Cheers...
(FYI his antivirus is off)..

Event viewer shows no errors, driver boost found 21 hardware drivers, mobo related, etc. outdated and they have been updated.
Faderport has been removed from control surfaces, unchecked in devices and physically unplugged.
No change.

Is there a way to log the startup of Sonar to see if it is getting caught in a loop and then giving up to proceed loading the app?

Remove all control surfaces and disconnect all MIDI and audio interfaces and then load. If its till taking long there is either some external service slowing down the load or its disk related. Try some disk benchmarks on the drive that SONAR is loaded on.

Noel Borthwick [Cakewalk]
Remove all control surfaces and disconnect all MIDI and audio interfaces and then load. If its till taking long there is either some external service slowing down the load or its disk related. Try some disk benchmarks on the drive that SONAR is loaded on.

I just started a backup since I want a drive image of my boot drive with all the new updated drivers installed.
I'll do as you suggest in the morning and report back, thanks!

Here is a good thread to read. 
http://superuser.com/questions/148824/some-apps-very-slow-to-load-on-windows-7-copy-paste-very-slow
 

Noel Borthwick [Cakewalk]
Remove all control surfaces and disconnect all MIDI and audio interfaces and then load. If its till taking long there is either some external service slowing down the load or its disk related. Try some disk benchmarks on the drive that SONAR is loaded on.

Removed all control surfaces, disconnected all MIDI and audio interfaces and tried loading, no difference.

Uninstalled Avast AV and after reboot, before installing MSIE, loaded Sonar, no difference.

No overclocking going on, big *ss noctua cpu fan installed and running so overheating is definitely not an issue.

Just benchmarked my os drive which is a wd caviar black sata with 32MB cache with CrystalDiskMark 3.0.3 x64.
Here are the results after 5 passes:
1000MB Test
Read [MB/s]     Write [MB/s]
97.88               93.63            Sequential
44.50               62.93            Random-512K
0.677               1.107            Random-4K
0.728               1.122            Random-4K QD32
 
100MB Test
Read [MB/s]     Write [MB/s]
129.8               81.16            Sequential
60.95               105.3            Random-512K
0.692               1.434            Random-4K
1.194               1.491            Random-4K QD32

When you installed X3 did you let it use the previous config? If so, you could try re-personalizing X3 by holding CNTL and SHFT when opening SONAR. This will overwrite all the files in your home directory\AppData\Roaming\Cakewalk\SONAR X3 Producer and make some registry fixes to bring your setup back to factory defaults. You could save off the user directory before re-personalizing if you want to refer to your previous settings.