Just thinking about this a little more - I am not sure that I really want to be able to manually adjust the delays; if I did have the option I would like to have an "Auto" setting.

Each processing block will introduce a delay, and that delay is probably fixed but might vary with a switch setting e.g. some of the flangers or chorus effects or just switching the effect on and off.

The delay for each processing block can be measured in "samples", so in Auto mode the sum of the delays on each path can be compared and the path with the shorter delay then delayed by the difference between the two to match the longer delay path.  

The delay may be different depending on whether the effect is switched on or off, but it shouldn't be difficult to update it in real time.

The same principle can be applied to the phase as well - each processing block models a real device that contains a number of amp stages, some of which will invert the signal, but the nett effect along each path can be summed and the shorter path inverted if necessary at the same time as it is being delayed (because even a simple inversion is going to cost a tiny amount of time).

Just an idea - my electrical engineering days are a long, long time ago; it is all IT these days