Of course methamphetamine being a base (pKa~10.4) at normal physiological pH (7.4) the equilibrium is shifted to the left. So, most of it exists in the plasma in the form of protonated METH (with the counterion being chloride or other anions in the body). Actually pretty much all of it is in the form of protonated: for 1 non-protonated (free base) molecule you’ll have ~1000 molecules in protonated form (3 log units difference between pKa of meth and plasma pH). So essentially there is pretty much no free base METH ("pure METH") once absorbed. This is true for the free base as well. Once absorbed (by eating or vaping) it will quickly get converted to the protonated form. That’s why you’ll see scientists referring to METH HCl (pure crystal) and METH only once in solution. Correct way will be to call it methamphetaminium (protonated form of methamphetamine with Cl counterion or others anions in the body like phosphate, sulfate, carboxylate...etc but mostly Cl as it is the most abundant).
As for binding/blocking of the Monoamines transporters in the brain which is the psychoactivity mechanism of stims, it is the protonated METH that binds and blocks them as you could imagine. Else, if that was the free base ("pure" METH) that is psychoactive, then you’ll have to smoke ~1000x more METH to feel the same effects (ie, you’ll need smoke 50grams of meth!!!!!??? to feel effects of 50 mg). And that is because concentration of free base is so low relative to the salt in the body/brain. Here is a pic of METH (protonated form) bound to the dopamine transporter DAT (notice the counterion is now a carboxylate part of the DAT protein: protonoted METH in green with NH2+ in blue and DAT carboxylate COO- in blue-red). Same things with the other 2 (NET and SERT).
Eh, maybe I missed something here, but I'm not quite sure how you arrived at the notion that there's almost no free based meth in serum once ingested, or that you'd need 50g of meth for the free form to be psychoactive?
Given the pKa of meth is 10.1 and normal blood pH around 7.4, it's pretty easy to calculate that around 6.3% of what's ingested should thus be expected to exist in its non-ionised form in serum at any given moment. That will vary somewhat over time as it distributes around the body (eg parts of the CNS, a few organs, lipid tissue and so on, which can maintain higher concentrations), but it's a pretty useful general indicator and not in any way insignificant.
As for the protonated forms being the main psychoactive ones, I think that's a bit of a stretch given they're not exactly lipophilic. How are they supposed to even reach CNS binding sites like that?