If you have it in you, do it after the written part of the program. If you are not opposed to being in the gym 5-6 days a week then do it the following day.
The written part should be done all at once. If you keep the rests short you should easily be able to do 29 in less than 2 hours, likely closer to 90 minutes. The weights and reps are fairly easy, you should be able to get by with 90 seconds rest on the work sets.
Changing form is up to you, I would recommend against it. What I like best about sheiko was the sheer number of reps. I thought of it as practice, repeating the same exact movement over and over again until everything was second nature.
Deadlift from pins is pretty much from just below the knee. Block pulls would work fine too but I would start them just a little bit lower (if the weight is enough to flex the bar when in sits on pins).
As far as maxes go, you can up them after every 4 week cycle if you like, just add 5% to each and keep repeating 29 until the month before you contest then switch to 32. I have both as excel spreadsheets where you just input your 3 maxes and generates the months worth of workouts for you. PM me with your email if you are interested.
Other Tips that I got from Eric Talmant and Dave Bates (his coach): The GMs should be at about 50% of your squat max, they should be restorative in nature. DB flies can be done on floor to prevent over extension and can even be replaced with db floor presses (I have a bad shoulder and couldn't do flies). Try to keep rest periods at 90 seconds for work sets (above 50% of max), you may even gain some conditioning. Wait until after week 3 to decide if you want to up your maxes, don't do it after week 1. And always round the bar load UP to the next 5 pound (or 2.5 kilo) increment! Because the weights are reasonable, every rep should be perfect. Remember this is also PRACTICE.
Good luck with it, at first glance, the volume looks crazy but in fact it is quite manageable. One could even knock 10% of his maxes for the first cycle of 29 to adjust to the volume then for the second cycle go back to the true max and work from there.