I wouldn't worry a bit about alkaloid content with rustica and flowering, once it starts flowering your best bet, in my experience, is to let it do it's thing. Rustica is incredibly potent, dangerously so, and flowering isn't going to effect the potency in any appreciable way unless you're growing it for insecticide or something. Also once it starts flowering, you might want to consider staking it up as the seed heads can get really heavy and will sag to the ground. I tried to remove flowers one year thinking it would up the yield but as soon as you do, it will simply flower at every node beneath the one you removed and good soil and insect control seem to be the only real magic involved.
I have a curing process I use for rustica and other tobacco that works really well and will produce a perfectly fine usable product in a matter of several days. I talked this over with some other tobacco farmers and they told me I was crazy, but it works for small scale production and really well for rustica. Harvest the leaves when they get as large as you want them to be, don't worry about waiting for the yellowing on the stalk. With Rustica, once I get a pretty good stack of leaves, I get a needle and thread and string them up with a little space between them to allow air flow and hang them in a shaded area with good circulation. Let them hang until they start to yellow and curl up, but way before they get brittle (this takes some experience, but 'moist' is better than 'damp' and 'wet' is ruinous).
Once you have them off the string, stack them up in neat piles, alternating as you lay them on each other, i.e. front to back, then back to front, and press them flat. Put them in a large ziplock bag, press the air out of it, and seal it up and put that bag on a heating pad with a towel for insulation and a fairly heavy weight like a thick book on top of it and set the heating pad on medium. Make sure you keep the heating pad on, the new ones suck for this as they shut off automatically.
Check them once a day, if you see water in the bag then you've put them in there while too moist and will need to take them out, separate them out and let them dry a little before replacing them in the bag and make sure you absorb the water in the bag itself. You will develop an eye for perfect moisture for this over the years. Over about two or three days, the smell of the tobacco will transition from a grassy smell to a sweet cured tobacco smell that is unmistakable if you're familiar with it and the color will give over to a deep chestnut color. When that happens, you're done and have cured tobacco in a few days as opposed to worrying about hanging in in a barn for months and trying to keep it in case etc.
Store it as you would normally, just watch the moisture levels as tobacco is prone to molds.
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