I'm not taking lessons right now but I did in the past. I studied classical for 5 years and moved on to jazz for 3 years, then I went to college, now I'm done and getting back to playing the saxophone but you're right, I think I just need to keep practicing long tones with a tuner. I use a Korg chromatic tuner and I also have the tonal energy app. I've just lost my embouchure muscle memory and I'm trying to get it back through daily practice. I just want to know I'm headed in the right direction. Thanks for your reply and advice.

1. Yes, I'm flat against a tuner. It's flat on the lower end, from low C to G. 
2. I'm playing a Vandoren V16 mpc. It's a 5 tip opening.
3. When I was in high school, I was playing a Selmer S80 C* mpc, I don't know the tip opening.
4. I'm using Rico 2.5, I've tried Rico 3.0 but it's too hard. I didn't try going lower yet because I've always used 2.5 strength reeds.
5. I am using good air support. 

Another remark: I played my horn earlier today. When I pushed the mouthpiece in with a 1/4 inch of cork still visible, I was in tune on the lower end, from low C to G, and the higher end as well. I noticed that the 2.5 Rico reed I was using already had an hour's worth of playing time, so the issue could just be the reed being too stiff and hard to manipulate. I might have to lower my reed strength or wet my reeds thoroughly before practicing. 

Sorry for wasting your time. I'm just trying to figure out how I can play in tune consistently. I just need to narrow down the variables.