My daughter was also an easy 2, but began to try and seize her independence at 3. What had worked before for us no longer worked! And I totally feel your pain on the whining - that really pushes my buttons too.
Here are a few things I learned, through books, a parenting class, and some trial and error. Perhaps some of them will apply to your situation:
Children need to be able to make some of their own choices, at a level that is appropriate for them. At 3, I picked out 2 or 3 outfits and let my daughter choose one. She was more cooperative in getting dressed then because I gave her an appropriate amount of personal power.
I also made her a morning and evening sticker chart. They were super simple, and I drew pictures instead of words (just stick figures, nothing fancy!). Morning tasks were brush teeth, get dressed, go potty. Bedtime tasks were brush teeth, pick up toys, put on jammies. She loved putting her stickers on and felt proud of her accomplishment. At the end of the week I had special sparkly or puffy stickers for the chart.
I joined the YMCA. The exercise and the time alone (I was also a SAHM) helped me keep my sanity on a regular basis, not just when my workaholic husband had time to give me a break. If I was really losing it (and sometimes I really was) I had somewhere to go to get the break I needed. I figured an hour a day away from my daughter was worth it if it made me a better mom and I felt calmer and happier. And I took her swimming afterwards - the water was soothing for her.
Also I started getting really militant about bedtimes, mealtimes, snacktimes, etc. My daughter gets really difficult when her blood sugar drops - I have to feed her something about every 2 hours. And she really needs downtime too, like reading quietly with mommy or coloring, especially if she has had a busy morning. The parenting class taught me to ask myself in the moment, "is she hungry? tired? overstimulated? needing my attention?". Too much sugar, or junky food with artificial ingredients, will affect her behavior too.
I hope something in there is helpful - I know what it feels like to be home alone with a whiny child! You are obviously a good mom who cares enough to seek solutions, so I'm sure your son will be just fine. Best of luck to you. :)