This video shows you how to remove a rear wheel on a bike with a internal 3 speed hub. The hub here is a Shimano Nexus hub. Not all internal hubs are the same, but there are some similarities. I hope this helps.
There is a lot of good advise here but something that was not brought up is the dropouts. If your road bike has vertical dropouts then you can't turn the bike into a true fixed gear bicycle. The dropouts are the slots that the axle of your wheel fits into. However if you have a bicycle with semi-horizontal or horizontal dropouts then you can convert the bike into a true fixed gear. As mentioned above, it will require a special type of wheel that you can thread a fix gear cog and lock ring on to. Unfortunately you can't use a hub with threads for a freewheel because if you try to skid stop you will unthread the fixed cog. If you are just trying to turn it into a single speed you can ignore the above information.
I agree with cityzen, but also derailleur hangers are often knocked out of alignment without the owners knowledge. Realigning derailleur hangers require special tools and a true rear wheel. If limit screws are not the problem I would check the alignment of the derailleur hanger by putting the bicycle in the largest chainring on the crankset and the smallest gear in the rear. Visually draw a line from the smallest gear and make sure the smallest gear in the rear lines up vertically with the pulleys in the rear derailleur. If it does not then you may have a derailleur hanger alignment issue. Other things that can cause drivetrain noise are a worn chain, bent derailleur cages, derailleur cable tension, and worn out pulleys on the derailleur. Good luck!