what are you going to use it for? are you gonna wheel it and scuff it up regularly? if not i would honestly pass altogether. if you are gonna wheel it and mess it up more, 6 tops i would say, 5000-5500 would be better. considering the amount of stock things missing, messed up, etc im guessing you are just going to keep finding more things like that after you buy it. how are the rear axle seals? i would take it to the nicest toyota dealership in the area and tell them you want to fix everything, they will find anything thats even halfway done for you so you know. then leave, but use their quotes that they gave you on the items as part of your low ball.
but in my experience people who cant bother to fix $20-40 things like wipers and antenna's probably didnt keep up all that well on the more expensive maintenance either. i would honestly pass and wait for a better cared for one myself, way too many red flags on this for me.
I am having the dealership check everything out Thursday if it has a lot to fix then I am going to pass. Ill use it for wheeling and daily driving. We agreed on 6400 contingent on a good report from the dealership.