Try soft scrub. May need to pull the water out to make it effective.
The smell is caused by bacteria which live on the urine. To remove this you need to thoroughly wash the toilet and the toilet seat with soapy water infused with the recommended (on the bottle) amount of a good household disinfectant. This process will remove the urine residue and kill the bacteria. This process needs to be done regularly (2 to 3 times a day in a much used toilet and at least once a week at home).
The toilet can be removed fairly easily. 1. shut off water supply to toilet 2. flush toilet to get most of the water out of the tank and bowl 3. with a cup or a wet-vac remove the remaining water from the bowl 4. remove the water supply line from the toilet (usually on the left side under the tank) 5. remove the 2 nuts from the bolts sticking out of the bottom of the toilet 6. lift the toilet off of the bolts and you're done The "hole" doesn't need to be removed. Simply cut your vinyl around the flange. be careful not to cut the hole too big so that it is concealed under the toilet when you place it back on the bolts. You will also need to scrape the wax ring off of the bottom of the toilet and off of the flange on the floor. You will need to install a new ring when you reinstall your toilet Hope this helps