If your ultimate goal is to untangle the 3 interleaved conditions, I don't think that you could reasonably achieve that by modeling the BOLD response at the condition level (the issue of handling duration variation aside). The reason is that the BOLD response varies substantially across trials, therefor simply modeling the BOLD responses at the condition level would not good enough to untangle the effects at the trial level.
On the other hand, beta series analysis is good for computing the inter-regional correlations with the estimated effects. If you're planning to provide the time series at each region as input for the "connectivity" analysis, I'm afraid I can't see any effective solution for that.
Gang