Welcome back 
It's good to increase your mileage slowly. For clipping in and out, I can't stress enough the importance of "confidence building" rides on a trail or in a large parking lot enough. My first real experience with clips was a bad fall and that's the advice I receive which "did it" for me. And if you don't really plan on going a lot of places or doing a lot of mileage and aren't too attached to the pedals right now, you can always swap them out for platforms and just get back into riding again before you put them back on.
For shifting, I find that when I move to a hillier place or get on a new bike, it's helpful to be "reminded" by the shifting of others of a similar fitness level. So, group riding has really taught me a lot about WHEN to shift. It calms me down because I am not thinking, "Sh*t, I need to shift NOW NOW NOW!", I just follow suit and do it. The other option is finding a very quiet road with hills so that you can get ready for it. Over time, you will get much better. It's just hard at first.
***proud Hoosier, statistics nerd, and mom to a headstrong toddler***
****one car family and loving it!****
Owned by:
Le Monstre Vert - 2013 Surly Cross-check
Chessie, Scottish Terrier
Bonzai, Catahoula Leopard Dog