[BarkingPup]

Having an unspayed female could be a part of the problem. Another would be any strays that he might see walking across 'his' territory. Perhaps try covering up windows and removing window perches for a couple months?

I highly recommend getting a pheromone dispenser or spray bottle. If you don't want the cost (at least, in Canada it costs a lot) you could also look for Rescue Remedy which you add to their water... although, I'm not sure how much it costs since I can't get it here.

Extra love and play sessions might help burn off some of his excess energy. Maybe add another litter box, just in case he feels threatened. Ummm, I think that's it. Good luck

 

[BarkingPup]

It could be either the neighbour's males (which he has fought with) and being unable to get to them from behind a window.

OR

Since he just started using a litterbox he could feel threatened by other cats scent in 'his' box. How many boxes do you have? Where are they?

The general consensus is one box per cat plus one. If space is an issue the bigger the better (I have two giant boxes for my two cats). Placement is also a large factor. Each box should be in an easily escapable place. When inside the box the cat should be able to see every entrance and exit so if another cat approaches they can quickly finish and be gone. Hoods, in my opinion, are unnecessary and can cause anxiety since the view is limited and one cat may surprise another just leaving etc.

You could also try cleaning the boxes thoroughly with some sort of enzyme cleaner to get rid of all the cats scents so they can reestablish the boxes with all the scents at once. Then, clean each box once or twice a day religiously. If it is, indeed, litterbox anxieties this could help.