St John's Wort Doesn't seem to affect CYP2d6, so you are pretty much in the clear.
However, it IS an inducer of 3A4, and one or two others, with chronic (or sub-chronic, like taking a moderate-high dose 3 days straight)
Amphetamines are partially metabolized by 3A4, but mostly 2D is responsible, it is the primary metabolic pathway.
So in theory, you could slightly decrease plasma concenctrations, but since it doesn't interfere with 2D, the effect wouldn't be major.
If your worried, simply taking a 2D inhibitor would more than make up for it. Say, half a gram of cimetidine. Amphetamines are very susceptible to such inhibitors, though I admit I know slightly less about methamphetamine, the metabolic pathways are the same.
For future reference, St Johns Wort interfes with a LOT of medications, and can really weaken drugs of abuse if you are taking it regularly.
Good Luck, anything else, ask away