I just played around a bit and noticed old comments appear when I sort my user profile by top or controversial of all time. Going do delete those manually tomorrow, though I have no idea if these are all. Comments are >4yrs old and definitely behind the assumed 1,000 comment limit.
You can get your top 1000 (only updates as comments are voted) your comteqverisal 1000 and newest. So you should be able to see your most popular. In theory if they were all different you could see 3000 comments but they is likily.overlap. Reddit doesn't bump any into new if you delete and doesn't go looking for votes on delete either.