Hi Bill, I'm not a bread machine expert by any means, but if you're letting the ingredients rest for 30 minutes it shouldn't hurt to mix them up until everything is moistened before beginning this cycle. Keep in mind, however, that fermentation will begin as soon as the yeast is moistened, so you'll want to include this "rest" or "autolyse" period in your overall calculations for rise times. I suspect when doing this you could eliminate one of the final rises (I think you can do this by selecting 0 for the time). You can also move the machine on after shaping the dough by selecting "start," so you don't have to allow the dough to rest for a full hour there. I don't think you should need more than 1 hour rise time after the dough is kneaded and another 45 minutes-1 hour of time after the dough is shaped before the bake cycle begins. More rising time or "resting" than that may result in overproofed dough that is likely to collapse during baking. 

I hope this helps! Again, I'm not a bread machine expert, so it may take some playing around with your machine to get the timing perfect, but I think your major issue is too much rest/rising time before baking. If you do convert that first rest into a modified autolyse by mixing up the ingredients, that's going to set the fermentation clock going, so you'll want to be sure to shorten some of the rise times later in the process. 

Barb

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