I parked my truck for about 2 days and it was fine when I parked it but when I fired it up it had this tick or knocking sounds, wanted to see if anyone else had the same problem. We think it's the timing chain since I got a bunch of misfire codes but any extra info would be a great help, thanks.

 

How many miles are on your truck?
Give her a bellyful of Techron treated gasoline and clean the MAF sensor. You might get lucky.

 

It's got bout 185,000 km on it, but since I bought it I've only ran basic fuel, I also put fresh synthetic oil about 10k or so ago

 

Techron is available in shops and frequently goes on sale here in the US. Many people swear it's an effective cleaner.
Add it before a stint of local driving because it works upon shutdown.

FYI: Also, many will say your gas filter is overdue for replacement since you're at 185Kkm / 116K miles, but that wouldn't create a misfire/knock/tick condition overnight.
After you chase down your condition be aware that the oxygen sensors and timing chain tensioners are 160Kkm / 100K mile replacement items.
These are "Crossing the T's and dotting the I's things" to be done soon after you address your current problems.

 

Let see, this a 2003 V6~4.0L~SOHC + 5r55e Trans + 1354 TCase +...
Yep, a Bottle of InjectorCleaner & Tank of PremiumFuel once\twice a year does help.
At 185kClicks\116kMiles, it's overdue for
~ new Left+Right OilPressurized TimingTensioners (NotoriousFailureItems)
~ new Plugs+Wires; Clean+OhmCheck the CoilPack, renew if needed
~ new OxSensors 3each; Bosch# 15719 with 24inLong Cable+Plug will replace any Ford 4WireNarrowband OxSensor
~ new PCVValve, MotorCraft# ev243\ev268; inspect PCVHose+Tube assembly (NotoriousFailureItem) for cracks+leaks, renew if needed
~ new FuelFilter
Click above links for more info.
Also, inspect KnockSensor under IntakeManifold with its Cable~HarnessPlug on right side of Manifold; could be damaged.
Various other items should also be serviced at 50kClick\33kMile & 160kClick\100kMile intervals.
Hope this helps.