There are way too many variables here for me to be able to offer a complete answer to your question, but I've researched the voyages undertaken by Dutch ships sailing from the Netherlands to the Far East via the Cape of Good Hope in the early modern era, and can offer the following general comments based on their experience – note that the basic design was pretty different to that of junks.

• While at sea, the average speed over a long voyage was about 2.5 miles per hour. That's for a merchantman, built for carrying capacity rather than speed. A warship would move at almost double that speed.
• Ships could sail on 24 hours a day, but the decision on whether to do this would depend on how open the waters they were sailing in were, and how well known. Sailing by night was, obviously, risky if there was any chance of moving into shallow waters, and if that seemed to be a risk, a master would heave to overnight and continue at dawn
• Currents and prevailing winds matter a lot. A ship sailing from the Netherlands to Java – a distance of 15,000 miles – would take about 18 months in the earliest period in which the voyage was undertaken, because they traversed the Indian Ocean against the prevailing winds. After 1610 a fast route much further to the south, taking advantage of a strong prevailing current, was discovered, and this cut journey time to just six months
• Ships carried a lot of salted provisions in their holds, and essentially could stay at sea for as long as their fresh water held out, but this was not at all comfortable – water quality deteriorated after the first few weeks at sea – and so they would put in to land where possible. In the Dutch case, they would typically stay at the base they created at what is now Cape Town for a couple of weeks before finishing the voyage. But if your voyage is only 3,500 miles, I'd say no ports of call would be necessary
• Your crew is way too small for a sailing vessel. Any vessel would have to carry sufficient sailors to furl all the sails on all the masts simultaneously and quickly in the event of a major storm, which was one of the biggest risks a ship would face. Then you have to factor in the need to have at least two, and probably three, watches. So, how many masts and how many sails does your ship have? A crew of more than 100 sailors would not be unusual for a medium size trading vessel on a long distance voyage; if your ship is a merchantman carrying cargo as well as passengers I would expect it to be about that size. But from your description I get the feeling you imagine it as quite a bit smaller than that, carrying no significant cargo. Even then, it would probably be undermanned with anything fewer than 30-40 seamen.
• You're also neglecting the need for specialists. Even a smallish sailing ship would need at least half a dozen officers and boatswains, a few carpenters, caulkers, sailmakers, cooks, and so on to keep the ship running safely and efficiently in addition to seamen.

Hi there - we're happy to approve your question related to your novel, and we are happy for people to answer. However, we should warn you that many flairs have become reluctant to answer questions for aspiring novelists, based on past experience: some aspiring novelists have a tendency to try to pump historians for trivia while ignoring the bigger points they were making, while others have a tendency to argue with historians when the historical reality does not line up with what's needed for a particular scene or characterization. Please respect the answers of people who have generously given you their time, even if it's not always what you want to hear.

Additionally, as amazing as our flair panel is, we should also point out that /r/AskHistorians is not a professional historical consultation service. If you're asking a question here because you need vital research for a future commercial product such as a historical novel, you may be better off engaging a historical consultant at a fair hourly rate to answer these questions for you. We don't know what the going rate for consultancy work would be in your locality, but it may be worth looking into that if you have in-depth or highly plot-reliant questions for this project. Some /r/AskHistorians flairs could be receptive to working as a consultant in this way. However, if you wish for a flair here to do this work for you, you will need to organize this with them yourselves.