The puritan/separatist dichotomy really isn't all that useful a concept in understanding the early colonists. It is true that a distinction can be drawn, but the Mass Bay colonists got along fine with the Plymouth colonists in terms of religion and church polity. Among the reasons for this may be that the Mass Bay people, while they said and probably believed that they did not want to separate from the Church of England, had in fact crossed the Atlantic and set up in the wilderness in order to do things their way. To say that they did not separate is something of a stretch, and they may have felt they had not separated because they felt THEY were the true church. The Plymouth separatists, on the other hand, were much less rigid about separation than often characterized. Pastor John Robinson, who stayed in Leyden until he died, characteristically looked for commonalities rather than differences. When the two groups found themselves close together in the colonies they quickly recognized that they were very close and often churches from one colony would ask for advice from churches in the other and ministers moved between colonies freely although there was an economic aspect to this too--Plymouth couldn't afford the "best" minsters.
Also Plymouth was a poor colony and went for many years without an ordained minister and when they did have ordained ministers they were almost always not on the same level as those in Massachusetts Bay. Some of the foremost puritan ministers in England found that for their health a voyage to New England was a very good idea, and so there were several high power ministers in Mass Bay who were pondering doctrine 24/7 and nothing like that was going on in Plymouth, so there was not the occasion for dispute.
This is not to say that everything went well between the colonies, but the differences were usually over territory, trading rights and Indian relations or politics having to do with keeping below the radar of the English crown, whoever that happened to be at a given time, and none of that really filtered down to the general populace.
The two colonies were less homogenous than sometimes thought, though. Individual towns were generally established by congregations or by business oriented partnerships who drew people from different parts of England, so that in Mass Bay even though two towns were next to each other, the cultures, especially in the first generation or two, might be very different. The New England culture also was very village oriented, unlike that say of Virginia, and that also tended to bring people together--literally in many cases where it was in fact illegal to build a home outside the small village and people had their farmland (pastures and hayfields mostly) outside the central village and away from the home. So the young people were growing up in close proximity and naturally that was the natural pool of prospective spouses. Of course, most people didn't get around much, which is to say not only were there forces pulling people together in the village, there were forces keeping them from going out from it too. Also, without any real social "safety net," it was important to consider who would take care of one's children in the event the parents died--so you often see siblings from one family marrrying siblings from another, and when marriage was also partially a business arrangement it was natural that the parents dealt with the people they knew well and had often grown up with in England.
There were a few families that had the money/status to live in a larger world than the majority of people, and marriages between people of Plymouth and Mass Bay were not uncommon among those people. On the other end of the social scale, where people did not have land to be tied to, there was more movement and more intermarrying, as there was also among those families whose members moved between seaports in maritime trades.
A book very often recommended for an overview of Plymouth Colony which also has a strong genealogical component is Eugene Aubrey Stratton's _Plymouth Colony_which can be purchased for about $20 or less when it is on sale which happens frequently, but which any library should either have or be able to get easily on interlibrary loan. That's a good starting point for Plymouth, but of course most of the people you're interested in are Mass Bay people, and I don't know of a comparable book for that colony. Perhaps because records have been so well kept, the Mass Bay colony is very fertile ground for PhD candidates writing dissertations. Consequently there is a vast supply of arcane books written in turgid academic prose and meant to impress a doctoral committee. These often look at the colony in terms of whatever happens to be the fad in the graduate schools at the time, and very often they look at just one village. So there's no shortage of books about Mass Bay, but the problem is finding one a person would want to read or which is a broad, non-controversial overview type thing (exactly what a PhD dissertation turned into a book is not). Francis Bremer wrote a biography of John Winthrop, _John Winthrop: America's Forgotten Founding Father_ , which was published a couple of years ago and is quite readable and should be available in most libraries or easily gotten. Since Mass Bay was very much Winthrop's baby this could be a good start, but of course since it is focussed on Winthrop it's not really an overview of the colony. Still, I think it would make a good starting point. There's a substantial amount devoted to Winthrop's life in England, but after all it was his life in England that caused him to lead a thousand people to New England and govern another nine thousand in the next few years, so it's not irrelevant to what Mass Bay was all about.
But the settlement of New England was much more complex than just being the story of two colonies. Even without thinking about Rhode Island, Hartford, Nantucket, New Haven and the settlements in what became New Hampshire, there were independent groups coming into both colonies and finding places to set up, and there were always those who were brought along as labor and so on. So it could well be that the individuals you're most interested in would not be part of the core of Mass Bay or Plymouth.
Finally, I would suggest that you might want to try some of the Rootsweb mailing listshttp://lists.rootsweb.com/
which are free and easy to get on and off. There is a huge number of lists, and a huge variety in the number of people subscribed and their expertise, but the Mayflower list has many people who can be of great help if you have questions relating to the Mayflower, and the county lists are also very good. Those under "general interest" for MA I feel would not be as good as the individual county lists.