4 rounds of standard manske and extensive filtration on ~6g of freebase alkaloids, and the final result was crystallized from salt solution very slowly. After the first crop of crystals about 6g(yellow color, only 1.5g pictured), the liquid was poured off and reduced, and filtered. Then, over 2 days these large orange-red crystals precipitated. Are these different compounds? Is the only way to separate the harmaloids by precipitating the bases at specified pH levels?

that's one way.

harmalas could be easily separated on strong cation exchange resin (H+)

Any idea which one is which?

How do you know this is fractional crystallisation? Colour differences does not usually tell you much.

I don't, that's why I came here to ask.

The topic title may suggest a separation of harmine, harmaline and THH, which is not the case here. But beautiful crystals!

I recommend the bicarbonate method for actual separation of harmine and harmaline.

you could try to figure out if they are different alkaloids; for example, when cooling your manske, you could control the temperature very precisely and separate the crystals by temperature fraction, then dissolve them and see what ph they precip at. Of course I've seen some evidence on the forum that the ph separation is not very effective itself, so you'd have a lot of stuff to work out to get any meaningful results.