sodium carbonate wash is good specially if separation of solvent from mimosa wasnt perfect and you feel there might be traces of the basified liquid there
hmmm.. 300ml isnt much water.. At least one problem I can see is, if its so concentrated like this, any small spill will mean a lot of lost alkaloids....
Personally I would reduce to maybe 500ml, but then you would have the problem of having to do two rounds on the separatory funnel. I think either way its gonna work fine actually 
As for the pH, truth is, you dont have to acidify much at all.. Even if it was, say, pH 6, it would already be enough.. Actually even if you didnt add any acid, the alkaloids should naturally be in a water soluble form so you dont have to worry about it. Just add a little bit of acid and thats enough. As a side question: why hcl? why not vinegar, if its food-safe and so easy to find and works just as well?
Yes you can boil MHRB on the acid step and when reducing.
Add NaOH till the solution turns black, and maybe a bit more.. Too much wont be a problem. If you have trouble with emulsions, just add plenty more NaOH or some pure salt, and this should get rid of the emulsions.
3x30ml seems very little naphtha.. Maybe better do, say, 6x30-50ml.. Freeze precipitation instead of evapping is recommended. Check this out for some tip on how to retrieve the crystals from freeze precipitation to avoid melting dmt problems. Dont throw your basified mimosa solution until you have yielded all your crystals, in case your yield is very small it might mean a lot of it is still in the mimosa solution
Shaking the separatory funnel might create some nasty emulsions.. you can add lye to break them but its definitely better to just avoid emulsions, and mix by stiring/turning over end.
You can both warm up just the naphtha or the whole thing, I dont know how much it matters, any of the ways will work fine... Just obviously take safety precautions like never heat a solvent with open fire, or dont heat anything in a closed container, etc.. Also be careful when working with lye, always used safety goggles and gloves.
good luck!