Finally had time to sit down and read through all the updates. My comments are below.
For the event tables, I think the bottom results of all the tables practically requires pre-spending Edge to avoid them.
As a whole, I think the list of house rules increase overall complexity, though that's not necessarily a bad thing.
I'm not entirely sold on the revised aging rules, but we discussed that in another thread (I'll mention here that at 46, I'm stronger, faster, and have more endurance than ever before in my life; aging is what you make of it).
I'm also not sold on the changes to Stage 3... what problem were you trying to address?
I thought you were going to add Protocol to the list of language dependent skills?
Did you reverse the base rules on Natural Aptitudes? I thought Complex skills were more expensive...
Toughness makes sense, but I think I would have left Fit a separate trait, but used the same principle.
For the SPAs, I think it would make sense to group the attribute linked ones together, vice making the reader sift through the whole list to find the CHA linked one. Also, it should be "Lightning Reflexes" vice "Lightening".
Similarly, I recommend grouping all the Martial Arts ones together.
I strongly recommend "Practical Experience" be more expensive. Taking the 2 best of 3 dice roughly translates to a +2.
Conversely, I recommend "Smooth Driving" be cheaper. It has a built in drawback, so no need to overly penalize someone for taking it.
I'm inclined not to comment on your AU specific rules, but I have to ask: with your changes to LRM-5s and LRM-15s, why not just make it half a ton per tube, and remove the restrictions on rack size? The cluster table has all the columns now, so it will support them. By assigning an appropriate (fractional) heat value to each tube and rounding up, you could easily yield the current heat values for the existing racks.