Devin,
After reading reading through all your posts my first thought was 'Welcome to my world'. I have had several 'issues' with my 4110 also, and the dealer has been less than helpful.
The growl, I believe, is normal. My 4110 growls and whines in some fashion or another whenever its moving. The first time I used a turning brake I thought the rear end was being ripped out.
The deck clearance issue was a real problem for me. It is the most aggravating thing about the tractor and I took an extreme measure to fix it - I put on bigger tires.
After my experiences I would not recommend one anymore, or any Deere product for that matter, but the 4110 fits my current specific needs fairly well. I actively looked for a replacement for a couple months but in the end I decided to keep it and live with the remaining issues.
Two features of the 4110 that I was unwilling to give up are the floating deck and the easy FEL mount/dismount system. The alternatives available in my area just don't have them.
Good luck and keep us posted.