If I recall correctly, he used the upper triangle of the connectivity matrix.

I am not aware of anyone who has used simulated networks and looked at directed connectivity. 

I don't think regressing out the task works particularly well as you are only regressing out the mean effect across all blocks, there will still be residual differences on a block by block basis that is in the data.

The WB option in the gPPI toolbox dramatically speeds up the estimation process, so you can loop through many seeds quickly.