Just from reading online I've run a bunch of programs--Malwarebytes (it removed 8 files last night), TDSSkiller, HJT. I went through and removed files manually and removed some in regedit, as well. IE is still redirecting, It appears it is still infected even in Safe Mode. HJT would not run due to it not being able to write to the hosts file. Malwarebytes does not find anything now.
I'm missing icons on my desktop and there is nothing under the start menu. After several hours spent on this today, I'm fairly frustrated.