You said you have had him 2 years and he is doing this today, but has he just started this or is this a continuation since he came to live with you?
I am no expert but I have dealt with some unusual behavior stemming from a fur kid's past, or from sudden changes like relocation, being dumped in the woods, etc. Unless you know something about what his previous life was like, it might be difficult to avoid creating 'similar' situations even if your feelings for him are wildly different from his previous owners'. Trying to avoid him being even remotely in a similar situation may help, if you can figure out a way...his reactions may help with that, and changing anything that seems to bring unwanted memories or behavior is beneficial. Also, just treating him as politely and respectfully as you would a traumatized human is helpful. Of course, shower with with affection,play time, and interaction whenever you can.
He may be 'marking' but if he seems to you to 'object' to his crate, blanket, and bowl from his previous life, why not take him to pick out new ones? Show him ones you like or think he'd like, and watch his reaction. Be sure to tell him how much you want him to be happy and comfortable in his surroundings and enjoy his stuff. If he likes a flatter bowl or plate, get it. If you have a flea market or shop at yard sales or thrift shops, take him and let him choose. He may just want a change. I know this sounds crazy, but all my kitties and puppies 'communicate' their wishes when I 'consult' them...and when I ask them 'which' they like or want, I genuinely 'expect' an answer.
If expense is an issue, put the items away and use something else you already have. Feed him on a small plate, put water in a soup cup or broad based mug, sit beside him while he eats. Offer him kibble a piece at a time, then lay it on the plate for him to pick up, tell him it's for him but you are making it easier or 'better' for him, then give lots of praise and love when he does eat it. Up the kibble count gradually when he eats it. Even though he's been with you 2 years, he may still have unresolved issues that your love, caring, patience, consistency, and training can help him to overcome.
Mine always seem really interested in things they want, and just give a polite passing nod or sniff to things they are indifferent about. I only buy toys 'they' want, unless something catches 'my' eye when they're 'not' with me...and they must look through all crinkly bags when I get back so there better be something in there!
I do hope and believe you can help him through this. It sounds like you really love him and want him to know his life is forever changed for the better with none of the worries of his past. Take care!