As you already seem to know, Safe Mode is supposed to eliminate all non-essential startup programs. If it runs ok there, then it might be a driver, or possibly a virus...
You might try running Malwarebytes to backup MSE. Some viruses can be seen by some anti-viruses but not others.
Do you know of any updates or changes to your system lately. If you watch Task Manager, do you see anything jumping on the CPU column?
You said you used msconfig. Did you try the the options on the General tab, or the boot tab and select base video? If you could get it to boot into normal mode with one of these things checked, you may be able to track down what might be inolved, starting from there.