Hi there. I'm Dr. Bryant. I've been practicing small animal medicine (dogs & cats only) for over 11 years. I personally owned a previously outdoor (rescue) cat that had the same problem, and I've treated MANY. It's a difficult situation. I'm sorry you and Sir Grey are going through this.
As you probably know, neutering is the easiest fix....if it works. Now you know that is not always the case (as it wasn't with my own rescue cat years ago). The remaining issue is purely behavioral in nature. Behavior issues are TOUGH because there are no quick, easy fixes. If you have multiple cats in or around your home, it is even more difficult.
The best advice I can give you is to keep multiple, immaculate litterboxes in the home (1 per cat, plus 1 -- i.e., if you have 3 cats, have 4 litterboxes) AND try to provide "environmental enrichment" for this cat. This is playing, petting/brushing, climbing towers, toys with catnip, laser pointers, etc. Things to "de-stress" him. Anxiety can be the cause (which is why your vet prescribed the amitriptyline, an anti-anxiety medication). Territory can also be the issue, which is why multiple litterboxes are so important. Sometimes, you can do EVERYTHING right, and still have a spraying cat. There is no guarantee. You just have to work your way through the many options for treatment.
Read these two articles for really good information and advise on steps you can take, as well as other medications that you may ask your vet for.
Just because the amitriptyline didn't work, doesn't mean another won't. My absolute favorite drug for this that works most reliably is Prozac (fluoxetine). It is my go-to drug that is always my first choice. I can't remember the last time I prescribed amitriptyline. The only problem with the Prozac is that it has to be compounded to be the right dose for cats. However, it is readily available in generic form, and compounding is pretty cheap and easy. There are national compounding veterinary pharmacies that will overnight it to you. You'll expect to spend $40-50/mo for this. It will be liquid or chews (your choice) and your choice of flavor. It only is given once daily. All things considered, I really like fluoxetine as a good solution when other non-medicine options fail.
Let me know if this information is helpful. If so, be sure to rate my answer. Good luck!!