You don't have a problem-----

there are a couple of things you can do to be able to get a 90 degree fitting end up pointing the way you want----in your case- maybe a smaller size npt and use an adapter bushing which would give you two sets of threads to use to balance out where the fitting ends up

If you take the 1/4 npt fittings you have(had) and use a couple of 1/4 to 3/8 npt adapter bushings you could tighten the combo to point the right way

When working with NPT pipe is takes an experienced pull/twist to know what is tight enough to work and/or can you turn it another full turn to still end up in the right direction.

Experience is a wonderful teacher if you can afford the tuition ( or so somebody said)