I have a similar case in which a participant got once a placebo and once a drug and then did two tasks [high and low]. The explanation here was very helpful in creating a design matrix, so thank you very much! My study has 32 participants and since every participant has 4 matrices, I created a 128x34 matrix. The first column codes drug, the second highVSlow and the rest indicate to which participants they belong. So the first 4 files belonging to subject1 would look like this: 

Sub1PH   0 1 1 0 0 ... 
Sub1PL    0 0 1 0 0 ...
Sub1DH   1 1 1 0 0 ...
Sub1DL    1 0 1 0 0 ... 

The permutation blocks would then look like this [1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, ...]

is this correct? (also see attachment) 

However, 3 things are unclear cause they seem to contradict other posts in this forum:

1. In other posts a column with only ones is additionally included to indicate a global mean. Why is this column here omitted? 
   
2. Similar to the post above, I encoded drug: 0 for placebo and 1 for drug. Why do other posts recommend 1 and -1? I guess there is a difference but I could not figure it out...
   
3. When I am interested in the contrast for 
   

main effect drug = [1 0 0 0 ..]  and for the decrease [-1 0 0 0]
main effect task = [0 1 0 0 .. ] (I guess this means high > low right?) 

I would run a t-test, right? And since I explore both drug > placebo [1 0 0 0 ..]  and placebo > drug [-1 0 0 0], I would need to half the significance to 0.025 to compensate for testing twice, right? Or would I actually need to divide alpha by 4 since I run both contrasts for both main effects to safeguard against alpha error accumulation? 

Thank you so much for your help! 

Cheers, 

Max