Some people get used to thin air quickly, some take longer and an unfortunate few can't acclimatize at all. A training plan has very little to do with that. It just takes time for your body to adjust.
Fortunately for you, the Inca trail is good preparation. If you can, try to add a night, or better two, at Lake Titicaca before traveling to Arequipa. There is no guarantee, but few people climbing Misti do more than that. Some do less and still get to the summit, some don't, and altitude sickness is the main reason for that. And most people are struggling with the altitude to some extent, including those that have been to Lake Titicaca.
Apart from the thin air, you obviously need to be in at least reasonable shape to hike up any big mountain, and if you are fitter, it will be more enjoyable. Personally, when I'm not in the mountains, I don't do all that much to stay fit. Roughly three times a week I do cardio. That can be running, at least an hour but very occasionally up to an hour and a half, or 45 minutes on the cross trainer, using an interval program. When I run, my heart rate is in the aerobic zone, on the cross trainer I push harder and it borders the anaerobic zone. In addition I do weight training, but you don't need that for Misti.