Thank you very, very much for your time and your analysis, Colin! It is massively appreciated and it's shed a lot of light on this for me! I'm still searching, and I don't know if I can put my finger on which one it is for definite.
I'm leaning towards it being either James Roy & Janet Ireland, or William Roy & Jean McCrabie. Although, I can't totally discount John Roy & Margaret Simson, I initially had it in my mind that having a kid in 1775 at 52 was a little late, but perhaps, considering it was his 3rd marriage, this wasn't as unusual as I initially thought.
It's very hard to pin any one down, and maybe I'll never be able to! All the names match up with each other (thank you again for that fantastic analysis!). John Roy & Margaret Simson have one thing going for them, though. Patrick Roy & Agnes Guthrie's first child was John Roy (as you said, probably named after his father). They only had this son, and then a year later, he married Hellen Jack, and they had a daughter called Ann (after Ann Guthrie, his dead wife, perhaps?). Their next daughter was Hellen, after his new wife, (and to even-out the daughters named for wives?).
Then, the next daughter is Jean; which would make sense if his mother was Jean McCrabie, but his sister (if he's the son of John Roy & Margaret Simson) was called Jean, perhaps that was after her? But then again, William Roy & Jean McCrabie had a son called John, too.
Patrick & Hellen also had a kid called William, which seems to only make sense if Patrick's parents are William Roy & Jean McCrabie; or, maybe Hellen's father was called William? But then why would Patrick wait to name his youngest son after his father? There was a Helen Jack born in Kilspindie in 1738 to William Jack and Helen Foord? But then again, there was a Helen Jack born to Walter Jack and Jean Dempster in 1731 in Perth, which might be more probable, considering her marriage to Patrick Roy says she's from that Parish. It would also explain their daughter Jean's name, without Patrick's mother having to be called Jean. That may have explained the William without the need for Patrick's father to be William.
It's all very confusing, and I'm rambling here, I know! I'm just torn between the fact that having Patrick's father called John Roy looks very likely, but the fact that they were from quite a distance from Perth. It clashes with the fact that James Roy and Janet Ireland were married in Tibbermore, and Patrick married Ann Guthrie in Tibbermore, could that tie in? I suppose it might just be impossible to tell, but I really appreciate your time and effort, Colin! These things can be so frustrating, and fascinating! Hopefully something comes to light!
Thank you very much!