Hi,
I have a 99 gt forester and want to put in a new turbo. I have a TD04-L off a 06 wrx. I know it's a lines up a little differently but just wondering if it will still fit?

Yes. Pretty common to fit td04s to replace the tf035 on the foresters.

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Doing it for all the wagons out there

Didnt GTs come with a TD04?
XT with the smaller one.

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Balls.

GTs came with a TF035 and XTs came with a TD04. I would consider both "the smaller one." Haha. BUT the GTs had the smaller of those 2 turbos. And also smaller engine with 2L vs 2.5L.

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Doing it for all the wagons out there

do yourself a favour and get a vf series turbo, also direct bolt on