For instance if a US resident is the sole owner of an LLC it will be a disregarded entity with no federal tax filing obligation, everything would be reported on the owner's personal tax return. 

It’s like having a disregarded entity, but has the possibility of different ownership structures for each series.

Not doing this can lead to fines, or, even worse, if the LLC is involved in a lawsuit, it can be disregarded because it is not registered to do business in the State.

If it is a disregarded entity, then all you have to do is nothing.

They also recommended to set it up as disregarded LLC such that taxes flow directly to your personal; this CA FTB never find out about the Wyoming LLC.

I have a Texas disregarded LLC, Oklahoma disregarded LLC, and Wyoming partnership LLC.

2) What are all the taxes (with rates) I would have to pay in regards to holding all my properties in a single-member llc (disregarded entity)?

For federal tax purposes the operating LLC is a disregarded entity.

I'm wondering if it would be a poor investment to disregard the 1% rule in this case?

To me that is a blatant disregard of his responsibility, and demonstrates how he would treat other 'formalities' like obeying a lease.