I’m afraid - this is gonna be really tricky. Amlogic Linux Kernel 4.9 tree is a vendor changed kernel and isn’t much the same what original 4.9 kernel was. Amlogic kernel had a lot of changes made, so RT patches against it will not apply cleanly… that is what patch is saying to you…
Hunk #1 FAILED at 39.
1 out of 1 hunk FAILED – saving rejects to file arch/arm64/kernel/asm-offsets.c.rej
…
1 out of 1 hunk FAILED – saving rejects to file arch/arm64/kernel/asm-offsets.c.rej
patching file arch/arm64/kernel/entry.S
Hunk #1 FAILED at 1764.
1 out of 1 hunk FAILED – saving rejects to file drivers/usb/core/hcd.c.rej
and so on… you can of course read what have been rejected and try to fix by yourself - but I bet won’t be much luck without knowing ARM assembly and platform details… Too much work in any case.
The only way you can go - is switch to mainline kernel and continue with RT patches… but you’ll definitely loose some functions - like MIPI - DSI output and some smaller features…