First off, strength training should be done before cardio, as you don't want to be fatigued when lifting weights. With increasing fatigue, your technique begins to suffer and you're more likely to get injured.
This is also why you should do compound exercises before isolation exercises, as compounds use multiple muscle groups and are therefore more difficult to perform right.
I also think you have too much isolation exercises in your program, which leads to a much too high volume. When training each muscle seperately you won't have the energy to give it your all across 52 sets.
With that said, a good beginner's full body workout should be done on 3 non-consecutive days per week and might look like this:
- Warm Up (this can be light cardio for 15min max)
- Squats/Front Squats, 3x5
- Bench Press/Overhead Press, 3x5
- Deadlift/Power Clean, 1x5
- Pullups, 3x12 (optional)
- Dumbbell Rows, 3x12 (optional)
- Cardio (running, elliptical etc.)
The warm up is more or less optional, as you'll be doing warm up sets before each compound exercise. It's good to get the core temperature up, though, and just warm up the body as a whole.
Now, the first portion of the actual program are compound movements, which you can alternate between from workout to workout. These are the most important exercises, as they train almost your whole body and will lead to more strength (and thus muscle) most efficiently. Since you're concentrating on technique and gaining strength, 3x5 reps would be optimal, hopefully allowing you to raise weight by 2,5kg (5lbs) per workout for some weeks.
I've found that alternating reduces the repetitive strain on certain muscles/joints and also shifts the work to muscles that would otherwise be underused. (Also note this is almost the basic Starting Strength program, which I can only recommend to beginners)
The second portion are auxilliary exercises. These are used to train weak spots that the compounds didn't cover. Once you progress and notice weak spots, you can customize these to react to shortcomings (Flyes for chest, Calf Raises for calves etc.). They are done to add volume to your workout, so 3x12 reps should be good.
Cardio is last, as it's not really that important if you're already exhausted when running. I assume you're doing this to burn additional calories and increase your cardiovascular performance. Thus, as long as you're not doing a running-technique session, being tired is okay.
I can't say much about nutrition, but if you want to build muscle (lean or not) you need to have a caloric surplus (eat more than you use). While beginners are to a certain degree able to lose fat and gain muscle simultaneously, that process won't last forever and it's inefficient. With a slight caloric surplus (~500kcal) you should be able to build muscle and gain strength fast, while keeping fat gains pretty low. Just try not to gain more than 0,5kg (1lb) per week and you should be good.