I can't figure out what I've read up to on Twitter anymore since it shuffles tweets around and inserts random "your follower also follows this person" tweets which I didn't ask for
If you turn off the "show the best tweets first" option in your content preferences you get a chronological timeline back. (They made this change a month or two ago)
Have you tried using Tweetdeck? It puts that kind of stuff in a separate column which you can show or hide as you wish. The main column is chronological.