I think Manaphy is method 1 because it's a gift. Sorry, but I don't remember stuff like that. I always look things up before an RNG project, even if I did it before. Most everything you need to find is on the first page of the help thread.
To get it shiny, you must use the SID and OT of a second game. Then you trade the egg to the second game, where it will hatch shiny. It cannot ever hatch shiny on the game that receives the egg. There's a code to stop it, but the code doesn't work on a second game that receives the egg from the first. All shiny manaphy must have link trade in the description for this reason, but it will still be treated as a hack on GTS and for wifi battle recording, despite that it was gotten legitimately in the game.
Pretty much everything for getting on delays and advancing frames is the same. The big difference is encounter slots. For every frame that has your target IVs, there is an encounter slot corresponding with a pokemon for the area you are in. It may not be the pokemon you want, so you have to check every frame where the IVs repeat until you find the right frame with the right encounter slot (right click the frame to see the encounter slot). Use sweet scent on a bicycle. You should stop two in front of your target frame instead of one. If you walk in grass, you will advance the frames as well, so hold still and use sweet scent (in HGSS).