Yeah, its been mostly miscommunication and a new and not very skilled manager. Thats why I am not planning to blacklist them unless things go south. I do think the feedback about legalities from this forum has helped a lot with sorting this out though. If someone went into the job with some Chinese skills, teaching experience, and an understanding of how things work in Taiwan they could probably avoid a lot of the problems I have had. Which have mostly been due to very poor communication. But it WAS wrong of them to ask for my passport/arc. As at the time I did not know that, I am glad to know what I ought to do and who I needed to contact. I think going in with my friend and having some information on hand helped a lot.
Any updates?
Not yet. I still need to file my taxes next week and get paid. They have stopped asking about the passport and ARC after I made it clear I would rather not give it up…Fingers crossing everything goes well. 
Well, here is an update.
Im getting things done, but no thanks to the management. She has let up on demanding my ARC and passport (She knows I wont give in.) But she has been a HUGE pain in the butt with giving me my paperwork to file for my refund, and even the tax office is getting annoyed with her.
When I showed up on Monday for my tax paperwork as we had agreed she refused to give it to me and said she could not give it to me till 4 working days before I left.
I had to go to the tax office and have the (angel!) lady there call her and tell her she HAD TO give it to me or they could not process my refund. After talking for a (long) while they agreed that I would get the paperwork for 2014 that day and then come again to file the paperwork for the 2 months in 2015 that Friday. That day I drove back and forth 3 or 4 times. What a pain.
Then, on the following Friday when she had told me I was supposed to file for 2015 she changed her story AGAIN and refused give me the paperwork for Feb till the next Monday. (Thats 3 days before I leave!) The tax office is pissed at her now, and they were all arguing about it since they now have to file 3 forms instead of one… and I have to make all these annoying trips when I’m in my last week here.
At least the tax angel saved my refund for me by demanding my boss give me my paperwork last week. If she had not, I might not be getting paid on time. … and its a big check! I’m happy I will get it. Thank you angel tax office lady!!! 
:discodance: 
I really hope there are no more struggles, but at least this makes a good story. I think I have managed (so far) to avoid serious problems mainly by being careful, doing my own research and knowing my rights… But its been waaaaay more of a hassle than it should be.
I have been very pleased with the tax office. I have also been very pleased with the ease of filing taxes in Taiwan.