1. Do not mess around with trying to get a JFRV through your son. Stay married until you can apply for and get the APRC.
2. You will tell your wife and assure her that you will agree to all of her terms for the divorce including custody and child support just so long as she remains married to you and assists you in obtaining your APRC first. If you are at 4.5 years of marriage, then you only have approximately 6 months left to go until you can apply for it. Once you have your APRC in your hot little hand, you will sign the divorce per WHATEVER demands she makes. Say it like you mean it, say it with a smile! You need to keep your wife happy and calm. Bite your tongue. Do not look for confrontations. Don't tap the snake on the head! Keep your eye on the prize.
3. You can continue to live it the same house with her until you get your APRC, or you can move out and get your own apartment. There is no legal separation in Taiwan. You're only married, or not married, so it won't effect your APRC application. I recommend that you stay in the same house for the next six months while you are applying for your APRC, as long as you can stand it and as long as you feel safe. Otherwise, find your own apartment in anticipation of what the divorce will bring anyway. If you do move out, you still need to pay everything and not assume or insist that she finds work. Keep everything on an even keel. Also, do not even think about fooling around with any other women until you are divorced. Again, separation in Taiwan doesn't mean squat and you don't want to face criminal charges for adultery or even worse, piss off your wife!
4. Make a quick trip to your NIA and see the agent in charge of the APRC applications. Tell them that you are coming up on 5 years of marriage very soon and would they please run your residency record to ensure that you are eligible to apply for the APRC and exactly what date are you eligible.
5. You should start working on your paperwork for the APRC now if you find out that you are eligible. You need to start with the police background check from your home country as that is the most time consuming part of the APRC application. If you're American, that means you need to do an FBI background check. No worries here because I've done 15 and helped other people numerous times. I've almost got it down to a science. PM me if you're American and would like assistance with the FBI background check. If you're not American, sorry you're on your own.
6. You need to ensure that you have reported and paid taxes on a minimum of $430,000 NTD for the 2011 tax year. This is the minimum for applying for the APRC. Tax time is this month (May), so be sure to declare and pay taxes on this miniscule amount if you want to apply for the APRC. If you decide to apply for the APRC after January 1, 2013, then you need to declare and pay taxes on a minimum of $460,000 NTD for the 2012 tax year. Oh...one more possible option for you. If you are a foreigner married to a Taiwan national, you can also show a bank account with a minimum balance of $500,000 NTD and can qualify for the APRC this way. However, the caveat is that the money has to be in the account for a minimum of one full year immediately preceeding applying for the APRC and the balance can't have dropped below this minimum during the entire year. See the APRC Application thread for more information.
7. Once you've gotten your APRC and the Open-Work Permit in your hot little hand, you can do whatever you want. Now, you will be in a position of power with the ability to negotiate yourself a proper and fair divorce deal with your wife. You can tell her that you've changed your mind and you don't agree to all her demands for divorce. You can refuse to divorce her, you can tell her you want full custody and you want her to pay you child support and she can have visitation rights. You can get a lawyer, waste tens of thousands of dollars and have a right proper divorce slugfest. The point is, you will have your immigration status already adjudicated, you won't need her assistance for jack shit and you won't be at risk for losing your status based on her attitude of the day!
I'm sure I speak for all of us when I say we are all behind you 100% and wish you the best during this most difficult time of your life.
Best of luck to you.