1. "What happens when you use just 000000001-1 for your glt, with max lag of 0, and the wavered input?"

In this case you simply make a comparison between the responses of the two conditions.

2. "What happens when you use 00000000111111-1-1-1-1-1-1 for your glt with a max lag of 5, and wavered input? Would all the results be useless or just the results for each time lag, but not for the LC given?"

I am not sure why you want to consider such a long lag in 3dDeconvolve with the wavered files since the hemodynamic response function type (i.e. gamma variate) you specified in waver already includes the response delay. If you have strong reasons for such a max lag, glt with 00000000111111-1-1-1-1-1-1 would basically give the significance of the magnitude difference between the two conditions.

Gang