If you are on windows, go to Your PC - C Disk - Users - "Your Name" - Saved Games - Pokemon Rejuvenation - Then copy the "Game.rxdata" file into the exact same location on your new PC.
Did you update the game in one of the areas mentioned here?
Do not load up in these locations:
GDC Interiors
Dream District Exteriors
Odd Path
Route 9
Odd Tower
Darchlight Manor (Backyard)
If the answer is no, try downloading the game again as some game components can be corrupted over downloads.
I suggest doing a completely new playthrough as it will be the final version of the game and minor changes are usually applied to early-game instances.
there is a link item obtained mid-way through the game before blackview city, just outside the small town. (Where there's an elder talking about trading)
The shiny rate is lower than Reborn and Rejuvenation, though I don't recall what percent exactly. You can find a guide for speeding up the game in the link below.