No you can't use the pokemon modifier, re battle or the blue orb to catch Kyogre on Soul Silver, because the game won't let you and it won't let you catch Rayquaza. Both Kyogre and Groudon must have been caught at the Embedded Tower, but you can use pokesav to generate a Legit Lv.50 Kyogre that have been caught at the Embedded Tower or use an AR code that lets you obtain a Kyogre that have been caught at the Embedded Tower in your PC Box. This code has been posted several times on a few threads by me.
No you can't trade a Shaymin from D/P/PL to HG/SS because it will not let you obtain the Gracidea Flower at Goldenrod City and even if you use an AR to obtain the Gracidea Flower you still can't use it on the Shaymin because it will say it doesn't have any effect. You must use an AR code to replace your first slot in your party. This code has been posted several times on a few threads by me. Also you can't use the pokemon modifier either.
I have tried every possible way to bypass this rule, but their is no way you can bypass this rule.