There's also nothing wrong with Qd1 playing against the new weaknesses on the d file.
Scotch Opening w/ Knight Exchange

Qd1? Something I didn't consider due to the fact that it puts white a turn behind, but I see it's merits.
5...c5? is bad too: leaves a backward pawn at d6 and a hole at d5.
5...d6 may be playable, but the centralised white queen is strong.
According to theory, 4... Nxd4 is bad.
Right. There is no knight exchange variation. I checked it up on lichess and less than 1% of masters have played it and literally every other move by black scores better than it - even Qh4.
Kind of funny how OP is sitting there wondering how come he now doesn't know what to do and feels like every move is bad when on the previous move he disregarded all theory to play a beginner move.
Admittedly this sort of tempo mistake, at least in more complicated positions, can get a little tricky, just think about how you're getting rid of your own well developed knight while bringing his queen to the centre of the board where it can't be attacked very well.
This one puzzles me. I always feel that c5 is a bad move positionally due to blocking the bishop and it seems to hurt the d-pawn. I'm never sure what to do with the queen, though.
I always think of Qc4, but then I expect the other person to take space by with a6 and b5 later, or maybe play d6 and then Be6. Qd3 seems like an option. Qe3 blocks the bishop some, but it doesn't seem like a bad option, especially since it's like the center game. Recently I tried Qd5, but that didn't work too well since Nf6 chases the queen.
Thanks for any help.