I'd just take a step back, a deep breath, and let your plants grow. Nothing looks seriously amiss here. The bumps on the stem are just where the tomato is thinking about sending out roots. Sunscald is a possibility for the yellow spots on the leaves, but the plant should survive just fine. Moisture stress (too much or too little) is another possibility, but not a serious issue. If you're plants aren't outside, and planted in a decent medium, disease is very unlikely.

I did begin the hardening off process

==>> explain this part ,... plz ....

ken

Hardening off means slowly introducing the plants outside, so they can adjust to the outside environment.