So sorry you are going through this....My thoughts are this is stress related cystis (another animal, territorial, etc.) or something in his environment that is causing him to pee outside the box. I am going to throw a bunch of things ot there for you to consider
I think the other posters gave some great advice as well that I strongly suggest you give a try as well.
You had mentioned that he is peeing on piles of clothes, etc. Is the house cluttered with many things lying around. Many cats DO NOT like clutter or anything lying around. Could you keep things off of the floor. Buy tall hampers with lids. Keep things in your closet with the door closed. My sisters cat did not like lots of things lying around (especially laundry) so he would spray on them. She finally stopped leaving much lying around and leaving everything in the closet with the door closed and this has helped tremendously
Yo had mentioned that you have perches for kitty to look outside. Do you have kitty condos for him to play on? Could you install shelves on the wall for him to climb on?
Since your kitty is peeing on soft surfaces I am thinking that maybe the litter is hurting his behind when he pees. He may not like the feel of the litter. He may want to pee on softer surfaces. Could you put a litterbox down with something soft in it like puppy training pads, a towel, newspaper, etc. to see if he will use this? Are the litterboxes big enough for your kitty to move around in comfortably? Is it covered? Some cats do not like covered litterboxes. You said that the cats only use one litterbox. Are both the litterboxes the same type? If you have to buy another litterbox you could buy a Rubbermaid container. They are much cheaper and you can get really big ones.
My sister had much success with a flower essence formula called "Spraying cat" from Anaflora http://anaflora.com/essences/index.html
I have heard that there are a few Australian Bush Flower Essences http://www.ausangels.com/contact_us.asp
which work very well on cats, who refuse to use their litter box: Billy Goat Plum, Rough Bluebell, Southern Cross, Sundew. Also, if you are buying the Feliway diffusers (my sister also has these plugged in for her stray cat and buys them in bulk). They are super expensive at the vets office here in Canada so what she does is buys them on different sites....http://www.entirelypets.com/6pakfedi..._utmk=24176955
, also off of ebay canada
With the exchange rate and shipping charges she still saves over $70 off of buying from the vets office.
I was going to recommend a product called Justrite to get rid of the smell and stains. It is an amazing product. Better than any product I have ever used. The only thing is it is only available off of the website and in the US. If you know someone that can get it to you from the US I would HIGHLY recommend this product. http://www.justrite.com/123kit.htm
Could you get plastic bed protectors for your bed until you get this under control? You can get them at Walmart, Home Outfitters, etc.
This could also be one of those cases where he wants to go outside so badly because he is always seeing the neighbourhood cats. And is very territorial. My girl cat is like this but thank god she does not spray. She does the motion of spraying but does not release any liquid. Taking him out on the leash supervised more often may help the situation
I think I covered what I was thinking....if I think of more I will post