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Glad you're playing around with VSIG and getting some use out of it! Sorry it took a while for one of us to respond.
Unfortunately switching the order of two effects within a single sigfile and completely avoiding any out of order modules is almost impossible. In your example if the Fuzz modules are ordered first, then placing a switch to move the Tremolo before the Fuzz will always mean the input to that switch (and therefore the whole Tremolo effect) will be out of order. The only way you can really do it and avoid all ordering issues is by having a second copy of one of the effects and then switching where the sigfile inputs/outputs are coming from/going to. For example in terms of module ordering your sigfile might look like: Fuzz1 > Tremolo > Fuzz2. To get Fuzz > Tremolo you send the sigfile input to the first Fuzz and take the output of the Tremolo. To get Tremolo > Fuzz you have a switch which then sends the sigfile input to the Tremolo and takes the output of the second Fuzz.
Hope that helps. This is unfortunately one of the trickier bits of VSIG as we don't have a way to on the fly switch the processing order of modules once the algorithm is being run (don't know if that would even be possible) so this workaround is the only one we really have available to us.
In regards to the second point. Comments in sigfiles are definitely something that's been on our todo list for a while. Just haven't had the time to be able to do it.
The VSIG patch sharing is a good idea and we'll keep it in mind.