Innapropriate urination problem

Question
Hello,
My cat has a serious problem with peeing where he shouldn't. He has a special affection for peeing on carpeting, beds (but not couches.. ) or particular soft surfaces.. So, attempting to remove the temptation, I moved him with me to a place that is all hardwood flooring. Additionally, I keep all beds covered with a plastic sheet, and he never goes near them after that.
He's been very good, going months with no major accidents. In the past week, however, he's begun peeing on the hardwood, randomly, with no real reason that we can nail down.
My new living arrangments include a large cat who very obviously runs the show.
This cat kind of terrorizes my cat, who seems to be filled with anxiety over the alpha.
As I mentioned, his peeing on the hardwood has only started in the past week, and there is no real catalyst that I can identify, besides the obvious ongoing emotional trauma of the bigger cat. (incidentally, the larger cat will be moving, with its owner in a month or two so that may resolve some of the issue.)

I took him to my local vet, who did a urinalysis as well as complete bloodwork, and my cat passed everything with flying colors. Phsyically, he is very healthy. So, this comes down to something that is very obviously behavioral.
My vet perscribed Amitriptyline in 5mg doses daily, which, to be completely honest, I will do because my cat seems like he's miserable, but i'm wary of how it will affect him long term.

I'm at my wits end, I don't know what else to try, i've done everything I could possibly do (in terms of switching litter, moving litter boxes, adding more, etc etc. ) and i'm worried that long term medication will first be horrible for his liver, and second, place him in a permanent medicated haze.

Sorry for the long back story, but what I would like to know is a) does this kind of medication generally require a long time to work.
b) does it require continuous use, or can it be stopped at a certain point, its behavioral changes becoming hardwired.
c) What kind of medical effects, (i.e. liver problems, etc.) could he possibly encounter...

and d) is there any other treatment, medical or otherwise, that could be useful in his situation.

I appreciate anything that you can tell me.
Have a great day.
Sonia

Answer
Hi Sonia!

BOY what a problem! I KNOW how you feel! One of my boys does this.

The amitriptiyline effects of the daziness do wear off eventually.  I would do bloodwork every 3 months when they are on any kind of behavior meds.  You can after a while decrease the dosage of the meds.

Ask your vet for a Feliway diffuser. ( you can get these in petsmart too I think)  that has helped my house in quite a nice way!

Hope this helps some!  Keep me posted!