Can anyone give me futher information on:
1) The relationship between the Presbyterians/Congregationalists non-conformists of the time and the Baptists of the time?
2) Can anyone explain the Refromed Baptist connection to the Reformation and Protestantism?
Up to the Great Ejection of 1662 in which many Puritan ministers had to leave the Church of England following the
Act of Uniformity, there were a lot of Puritans in the Church of England who wanted to reform it from within. After the Restoration of the monarchy, my recollection is that Presbyterianism eventually disappeared for the most part in England (merging with the congregationalists at some point If I recall correctly) and was chiefly confined to Scotland and Ulster (Northern Ireland.)
After the restoration of the monarchy, Presbyterians, Congregationalists/Independents and Baptists in England were all categorized as Dissenters and Nonconformists i.e. Protestants outside of the Church of England.
My guess is that most Baptists of that era either came out of the Church of England or came from the ranks of the independents with whom they shared the ideas of congregationalism and independency. The 1689 Confession is even closer to the Savoy Declaration of Faith and Order (a Congregationalist confession based on the WCF) than it is to the WCF. You can compare the three confessions side by side here
http://www.proginosko.com/docs/wcf_sdfo_lbcf.html
I don't know that there was any significant Baptist movement in Scotland until the 18th century.
In the USA, the number of Baptists started to grow rapidly as a result of the First Great Awakening. George Whitefield's comment on this development was “All my chickens have become ducks!”
The fact that the Particular Baptist confessions (both London Baptist Confessions If I recall correctly, certainly the 2nd) took paedobaptist Reformed confessions as their starting point shows their relationship to the Reformation and Protestantism. While Baptists share the idea of a "gathered church" of credo-baptized professing believers and a separation of church and state with the continental Anabaptists, there doesn't seem to be any organic connection with the anabaptists, especially as far as the Particular (Reformed) Baptists were concerned. The 1st London Confession (1644/1646) explicitly denied that they were anabaptists. This strong denunciation probably was related to anabaptist notions of pacifism as well as heretical beliefs held by some of the anabaptists.