You're routines should incorporate lots of running, skipping, shadowboxing/bag work, and bodyweight exercises, with some weight work. Cardio is very important in lasting the entire round, which is where the running and skipping comes in. In my opinion, sprinting would be better than jogging, and then do some skipping afterward for 30mins to an hour so you get two different kinds of cardio in. Shadowboxing is almost interchangeable with bag work, because both get you working on your technique, which is also very important. Treat any technique work like a fight, going for three minute rounds with minimal break to almost "simulate" a fight so you're conditioning is up to par. Following this, you should try to include LOTS of bodyweight exercises, the best being push ups, chin ups, and any ab work really. With just a medicine ball, ab workouts and push ups can be increased in difficulty greatly. The Chin ups are to help develop strong back and lats to help with punching power, and to mainly improve overall fitness. When performing any reps, try to make them explosive (ie clapping push ups and chin ups) so that you get used to exploding rather than just moving through the repetitions slowly. There's nothing wrong with performing them like that, but explosive is going to help you more in muay thai. Finally, weights can be included if you have them to help build a lot of strength on your body, and can really help you cut or gain weight. Just simple deadlifts, squats, bench presses, and light dumbbell work will really help you gain great strength, and the other exercises will help improve power. Hope this helps
EDIT- stretching should be after you warm up, after you shadowbox, and after you're completed workout. Even when you're watching TV, during commercials you can try stretching lightly, but don't overdue anything because if you're muscles are cold then you are more prone to injury. But stretching as much as possible is very very helpful!