I'll try to answer these questions as best as I can for as far as my knowledge goes.
1. You can add them all to one single pot (or two single pots, depending on your choice on question 3: one pot containing the vine extract and one pot containing the chaliponga extract). All three brews are just a part of the one brew that you'll be drinking and need to be mixed anyways. I don't see any possible negative effects from mixing them on-the-go.
2. I need to note that a lot of people feel the vomitting is an essential part of the ayahuasca experience. It is the fysical methaphor, so to say, of releasing your bad energies/demons/negative stuff. In my one experience with ayahuasca, one of the things that I found negative about this experience is that I didn't vomit. After reading a lot about it, I felt the purge belongs to ayahuasca. Because I didn't vomit, I felt I didn't really experience the true ayahuasca experience.
To counter what I just said:
Actually I do believe experiencing ayahuasca doesn't have to include vomiting. I do think that the fysical methaphor isn't needed to let ayahuasca be able to release these bad energies.
I haven't heard of peppermint being anti-nauseauting, but have also never really looked into this kind of stuff, so it could definately help. About the timing I have no clue.
I have heard about ginger being really effective. From my research back then, I can recall that at least one person adviced on chewing on whole ginger after drinking the brew or chewing on whole ginger when the first nausea comes up. I can't really recall which one it was.
If you really want to avoid the nausea, I believe I read somewhere on this forum that well produced pharmahuasca doesn't make you nauseated at all. Maybe you should look up something like this in google: "ayahuasca purge site
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mt-nexus.me" (without the quotation-marks)
3. The reasoning behind drinking the vine-brew and the chaliponge-brew seperately is that you first want your MAO's to be inhibited, before you ingest the DMT. If these are not inhibited at the moment they can reach the DMT, an amount of DMT will be broken down by the not yet inhibited MAO's. Some say this amount is insignificant or even nihil. I don't know if any definative research on this is available. Otherwise, I would take into consideration that there could be a significant amount of DMT be broken down if you don't drink them seperately. Thus I would then advice to drink them seperately, spacing them apart about 10 to 20 minutes. (First drink the vine-brew, then the chaliponga-brew)
As far as I heard long brew times do not have a significant negative effect on the potency of both the MAOi- and the DMT-containing component. One (seemingly experienced) person on this forum told he always does 5x5 hour brews, which are always potent.
I wished that I could give you more precise answers to these things, but I lack the experience and the knowledge. Also, as far as I know, there is no one right way of brewing and drinking ayahuasca. You should listen to the advice that suits you best and try that out. If, afterwards, you feel you have to change something, change it and then try out that different way.
Have a lot of luck, and also a lot of fun while brewing and drinking!