Hi jako, welcome to Thunder’s Place. :)
Don’t worry about LOT. It’s mainly for hangers and is about ligaments. Your best bet for now is the Newbie Routine. You can read about LOT, but several guys here don’t think it’s really valid.
1. Should I jelq in an upward motion, or side to side or just straight down?
Jelq in the manner most comfortable. Most guys do it straight up or out. Some concentrate pressure on one side or the other if they’re trying to fix a lateral curve (personally, I’m not sure that works since few, if any, have reported success). I don’t know any reason to jelq in a downward manner.
2. When stretching should I be holding towards the base of my shaft in an upward , side to side or straight down?
I think most guys grasp just behind the glans (head) so they can pull on the corpora cavernosa (main erectile chambers) as well as the skin and ligs. You’ll probably pull skin at first, unless you’re normal (uncircumcised), then your skin is probably loose enough to not be a problem. I suggest manual stretches be done in five directions. Up, down, left, right, and straight out. Follow the newbie routine for timing.
3. When stretching, if from the base, do I try to stretch the skin also?
I guess some feel that stretching only from the base targets the ligaments better, but why not let the stretch work on the whole penis? If one was to stretch from the base then I’d think stretching the skin would be unavoidable. You’ll probably have better results (that is, gains) if you stretch the whole penis.