Hi Aerus and welcome to Smogon!
I'm glad that you've started to RNG abuse with Heart Gold because it's very easy to start with when compared to much more tricky DPP RNG Abuse.
However, it's very hard to tell what you've done wrong without more detailed information about your RNG abuse progress (aka screenshots from RNGReporter, are you using any timer for soft-resetting etc.).
Anyway, I highly recommend to watch this video for HGSS breeding:
http://www.youtube.com/watch?v=El5VZ2OMEPU
1) You've found your calibrated delay/second which makes things easier. But instead of frame 3, you should search for IVs from frame 1 (set min/max frame to 1). That way you don't need to do any advances. Same goes for the nature/shininess: Start searching always from frame 1. Set higher delay range if you don't get any results (use EonTimer to hit your target delay).
2) See 1.
3) On Shiny Egg tab there's a filter option which allows you to search for seeds that produce baby pokémon with nature/gender you want most. You can check the gender ration from bulbapedia/serebii.
4) RNG Abuse Breeding of HGSS games has 2 steps:
1. RNG Abuse of IVs
You save your game in front of the Day-Care-Lady with both parent pokémon in your party. Then you hit your target time and verify that you've hit your seed with Elm calls/Roamers (Yes you really have to show Togepi for prof. Elm, visit Kanto region and have pokérus infected in your game).
Once you've hit your seed run around until Day-Care-Man has the egg and save in front of him. Take the egg, hatch it and see if it has correct IVs. Then you can turn the DS off without saving.
2. RNG Abuse for Nature/Gender/Shininess
You need to find a new seed for nature/gender you want and you will use the Shiny Egg tab (4th Gen Time Finder) for that. Hit your new Seed and verify it with Elm Calls/roamer method. If you hatch the egg and it has correct nature/gender/is shiny, congratz, you've done everything right. :)