1. I don't know if i didn't understand or if it's a mistake, but on the period of Mid Season (March-April ), on Wednesday the 4th and 5th exercise are exactly the same ( 8 x 100 short hill runs speed fast/rest walk back ) ( if it was the same he should of write 16 X 100 short hill ….).
I suspect it is a typo. I think the 5th exercise is just a duplicate and it should actually just be 8 x 100m.
2. how much rest do they take between exercise ( for example between 3 x 300 Speed 50 sec./rest 1 minute and 5. 3 x 300 Speed 40 sec./rest 5 minutes ).
I don't know. Seems like they aren't so much sub-sets but rather a continuous workout where their isn't a special rest interval between sets.
3. this program is done with shoes or spikes
I think they often wear shoes. In fact if I recall correctly MJ had a special training shoe-spike hybrid made to wear for these workouts.