My timer is not outputting when it should be... dont really know how else to explain. The dial thingy goes past the torch and a bit later, it actually fires the redstone...

Also, the timing doesnt really seem to be what I set the timer to but that may just be me...

It could be just lag. Have you got a decent PC/Laptop?

Yeah, my game supposedly runs at >300 fps with mods...
Its not lag

Could be a client/server-desync, client is rendering a bit to late maybe...

It shouldn't desync... once every 20 seconds it should sync the server with the client...