While I am certainly not at a definitive set of references, here are a couple which may be of some use covering 16th through early 18th century ship building (note some are contemporary, and others modern archeological or academic research).
This first discusses some of the 16th century Iberian ships.
Oertling, Thomas. 2001. “The Concept of the Atlantic Vessel.” In Proceedings. International Symposium on Archaeology of Medieval and Modern Ships, 233–40. http://www.patrimoni...arqueologia/18/
This next, while not concerning British shipbuilding, has some wonderful comparative photos and descriptions from less studied traditions.
Green, Jeremy. 2001. “The Archaeological Contribute to the Knowledge of the Extra-European Shipbuilding at the Time of the Medieval and Modern Iberian-Atlantic Tradition.” In Proceedings. International Symposium on Archaeology of Medieval and Modern Ships, 63–102. http://www.patrimoni...arqueologia/18/
For a very detailed description of Whole Moulding, Richard Barker has several publications, including the following:
Barker, Richard. 2001. “Whole-Moulding: A Preliminary Study of Early English and Other Sources.” In Shipbuilding Practice and Ship Design Methods from the Renaissance to the 18th Century: A Workshop Report, edited by H Nowacki and Matteo Valleriani, Preprint 245, 33–65. [Berlin]: Max-Planck-Institut für Wissenschaftsgeschichte. https://www.mpiwg-be...prints/P245.PDF
Realizing that the Mary Rose is about 200 years earlier than the period of interest, I still offer you the following:
Barker, Richard, Brad Loewen, and Christopher Dobbs. 2009. “Hull Design of the Mary Rose.” In Your Noblest Shippe. Anatomy of a Tudor Warship Archaeology of the Mary Rose, edited by Peter Marsden, 2:34–65. Portsmouth: The Mary Rose Trust. https://www.academia...f_the_Mary_Rose
Very brief, yet well researched, analysis of shell first/frame first and ship design, along with hull analysis information.
Olaberria, Juan Pablo. 2013. “Hull-Shape Design in Antiquity: How Do Archaeological Ship Remains Enhance Our Understanding of Hull-Shape Design in Antiquity?” A dissertation submitted in partial fulfilment of the degree of Master of Arts in Maritime Archaeology by taught course., University of Southampton. https://www.academia...rs_Dissertation
For those seeking much more detail concerning current trends concerning the historical ship building processes:
Nowacki, H, and Matteo Valleriani, eds. 2003. Shipbuilding Practice and Ship Design Methods from the Renaissance to the 18th Century: A Workshop Report. Preprint 245. [Berlin]: Max-Planck-Institut für Wissenschaftsgeschichte. https://www.mpiwg-be...prints/P245.PDF
Bellabarba, Sergio. 1996. “The Origins of the Ancient Methods of Designing Hulls: A Hypothesis.” The Mariner’s Mirror 82 (3): 259–68. doi:10.1080/00253359.1996.10656602
The Dartmouth is a very pertinent shipwreck -
Martin, Colin J. M. 1978. “The Dartmouth, a British Frigate Wrecked off Mull, 1690 5. The Ship.” International Journal of Nautical Archaeology 7 (1): 29–58. doi:10.1111/j.1095-9270.1978.tb01044.x
Which features in the reconstruction of a ship based on Sutherland's early 18th century treatise.
Kenchington, Trevor John. 1993. “The Structures of English Wooden Ships: William Sutherland’s Ship, circa 1710.” The Northern Mariner 3 (1): 1–43. http://www.cnrs-scrn...nm_3_1_1-43.pdf
Whew. Those ought to keep you occupied for a bit. Each offers a glimpse into either evolution of traditional methods or the identification of methods from field analysis of contemporary wrecks. Ultimately, when assessing the value of information (items) for understanding how things were done, there are many things which can be studied. Each type of item brings with it caveats concerning the validity of the information for drawing broader conclusions. In general, written treatises from the period are relatively reliable, if not always particularly illuminating (and clearly written). Anecdotal accounts (diaries, logs, letters &.c.) are less reliable but often can aid in ferreting out details. Contemporary models, while helpful, do not always reach the level of accuracy desired to understand how some particular aspect was accomplished, and also may not always show the accurate as built vessel. Drawn ships plans are perhaps more reliable, although rarely is the detail of deck features and arrangements included. Likewise, there is the as-designed and as-built dichotomy to consider.
Perhaps the best resource, when it can be found, is the remains of a given ship. With all the caveats concerning the changes in a ship over time (See the American Frigates Constitution and Constellation, as well as HMS Victory for obvious examples of well studied there to see ships which still spark amazing discourse over what was there in some prior century), a wreck analyzed and documented in situ allows a glimpse into how a ship was actually built which can surpass any of the other information sources for accuracy and detail, yet at the same time can leave so many questions due to the decay and loss of material.
At any rate, please let me know if any of these prove useful.
Kind Regards -