If you are going to do a linear progression, you might as well just do something simple like Starting Strength. By only doing deadlifts and bench right now you are neglecting your squat, which you could be improving at the same time. If you are making constant gains then you probably don't need to be cycling lifts just yet.
Unilateral exercises are extremely uncomfortable but they do help get you stronger and they address imbalances in the main lifts (i.e. one leg working harder than the other in the squat). Find ones that DO work for you body, and do them until they don't give you any benefit anymore.
As far as amount of weight each time you progress goes, just do whatever you think you can do. If you can make a 25lb jump, go for it. If you can only do a 2.5lb jump, then so be it.
I don't understand what you mean by the calorie thing, but I'll try to make this as simple as I can. If you used to eat like shit and you clean up your diet, you are most likely going to lose weight. As a general rule of thumb, the more you eat, the stronger you will get (assuming you are eating the proper amount of macro-nutrients). Very rarely will you be able to get stronger while losing weight, but it does happen on occasion. If you are extremely obese, lose some weight before trying to put on muscle mass. If you have a bit of body fat and are not worried about appearance, start putting on muscle mass then try and lose the excess fat later.