I've done Indigo a couple of times so I'll tell you what I've done
1) Increase the weight by 10lbs each week don't reset or re test. if you start with 225 then week 2 is 235 week 4 is 245 and week 4 is 20lbs increase so 265
2) Its up to you homes. This is a incredibly brutal workout. I would take a de load week if you're not an advanced lifter. This workout kicks my ass every time I do it. After 4 weeks my body seems tapped and take a de load week.
3) You can pick any leg exercise you want really. The extended sets might get difficult with single leg exercises though. Front Squat can be sub for leg press too. Just stick with the exercise for the four weeks
I would recommend doing just the frequency phase first for 4 weeks. If you feel good then add some pump stuff after the workout. I can't stress how much this can kick your ass if your diet is not on point every day, every hour, every meal.
This is by far my favorite workout I've ever done. No workout gets the same results
That said there is some guidelines that I've learned doing this.
Do a 3 on 1 off 2 on schedule. Don't do all 5 workouts in a row. Take a day off on the lat/arms day. It helps recovery.
FYI the first time I did this I killed myself after 2 weeks. You might think oh i can add some flies and the end of the workout I'm feeling good. Nope. Don't do it. You're benching/squatting/pressing 4 times a week. Gains came better when I put all my emphasis on my frequency lifts. Let the frequency not the volume take care of itself. And don't do the spec workouts. You're gonna over think it. you don't need them.
The only thing I still have trouble with is the dead lift day. Last workout of the week is dead lift. After squatting 4 times a week my dead lift wasn't really feeling good. So I switched to Chin Up day instead. Try the dead lift first but I suck at it. My arms are to short and it puts me a really bad position to start to I typically skip deads and focus on squats.
If I'm missing something Coach Thib/sensei could probably add like a million things to my list.