Seems like the standalone version ate my ability to take print screens (must be a java quirk or something), but oyu can find everything now under
settings -> SM/EC/EPI correction -> registration details and etc.
Pretty much everything should be there or under a slightly different name, with sane default parameters which should satisfy most use case.
For the gaussian smoothing, if the screenshot is form a really old version, it was moved under plugins, but alexander once said it also fell into the old pile of stuff which is still there for historical reason and should not really be used anymore.