Nice to see this coming along so well. =) In reading through this, I did notice the loss of alchemical bag content several times before, as well, across different versions. The one thing in common when it happened was that it was sometime after a black hole band was placed in an alchemical bag (sometimes much later). I remember trying to figure out what triggered it, but I never did nail it down, and no irregular messages ever appeared in the console. =\ For now, I would advise against putting the black hole band in a bag.
One little thing I noticed was how the gold horse armor emc was not in keeping with the other horse armor values.. the other horse armors seemed like they were worth 5 ingots/units of material, but the gold one is 1/2 an ingot worth.. I think Moze must've left off a zero on the end by accident, lol.
A bigger concern is the function of the watch of flowing time. I don't know how close to the original this mod is meant to be, but this is a pretty glaring exception. I remember the original giving a boost to nearby ee2 machines when active in the hotbar, at up to a 30% speed improvement, with a step of 10% for each charge level. For each one on a pedestal, it would provide a global 10% boost to emc machines (and it took like 31 or 32 pedestals with watches to reach the 10x speed-boost limit, iirc).
With the one in this version giving bonus ticks, even when held, and affecting all nearby functions (not just the mod's devices), it's way more powerful (not even comparable, really), and with the running costs being cheap compared to what it does, it's trivial to exploit. It seems the running costs are more in line with the original behavior and not this one, lol. I remember testing it once, starting a world with just this mod and nei and getting up to the point where I could make a watch and a collector. I started by upgrading fuels with the watch active and was able to turn a profit from just that. In a total of like 2 or 3 hours from the start of the world, with just building emc flowers and having the watch going at full power, I had full gem armor and an alchemical tome. I don't think it's an exaggeration to say that this is completely broken, lol.
Also, I could be wrong, but the emc running cost for the harvest goddess band when it's active seems abnormally high when compared to the original.
Anyway, just bringing up my concerns.. I'm sure people have already brought up the subject of the watch, heh. I still enjoy the mod and appreciate all the work that has gone into it and continues going into it. =)