All three have Gen 4 only moves. Flygon and Gliscor with Roost, and Lucario with Ice Punch. If you wish to keep the moves they must appear as tho they were transferred with the poketransfer.
I would start by using Pokegen its way more user friendly. As for the PIDs simply leave it blank in pokegen. Pokegen will automatically create one for you. The guide here http://projectpokemon.org/forums/showthread.php?14026-Guide-How-to-generate-Gen-V-Pokmon-in-PokGen should have all your answers. Oh and as for time it should only take a few minutes tops if you have all you info.
Well I just make your exact Garchomp with everything the same except id, sid, ot, happiness and I was able to get in just fine. So I have no idea what is going wrong for you.
Then try this. In Desmume start your game then go to file then click on export backup memory. That should make a .sav file then simply open pokegen 3.0b21 i think it is and load your save and you should be good to go.
You need to convert your save file in this case .dst or .duc to .sav format. The link here should have everything you need to do this. http://www.shunyweb.info/convert.php or http://saves.uniquegeeks.net/g/index/page.aspx?id=16
The GTS thread can be found here http://projectpokemon.org/forums/showthread.php?13834-5th-Gen-GTS-Research
As for editing Pokemon, Pokegen is by far your best bet.
Pokegen can be found here http://projectpokemon.org/forums/showthread.php?6424-Download-link-and-information
Unfortunately, I get stuck on a white screen after the Pokemon Showdown part. I have tried my own dump and its still a no go. Idk if it means anything but im on a scds2
Edit: Reformatting seems do have done the trick. So far its very impressive.
You have to make sure the game id matches the rom in R4CC. There should be something like "..." click that then select your rom it should get the game id for you.
Just downloaded your program and I think I found a bug or something. When I click start GTS everything works as it should, but when I stop it and start it again I get a System ObjectDisposedException. Only way I seem to be able to fix it is to restart the program other then that its pretty impressive.
It does that because the pokemon you traded over was a pc pokemon, if must be a party pokemon. I got a 255 Starmie once lol. To fix this get the seal case at the miltank farm in HGSS not sure about the others or trade it with someone that will remove the ball capsule.