Frank Fox is the reigning expert about English ships from the 17th Century. I will try to paraphrase some of what he has said about English ships:
With respect to armaments, the official establishments can't be relied upon. They weren't followed for various reasons, often the availability of the needed guns. Real surveys are the only thing that can be trusted. Some of those were published in Adrian Caruana's book, History of English Sea Ordnance, 1523-1875, in the first volume. The guns used included the light-weight "drakes" and "cuts", for demi-culverins, sakers, and minions.
With respect to manning, both the English and the Dutch wanted to man the guns on both sides in the first two wars. They allocated fewer men per gun than in later times. The establishments in the first and second wars are minimums. If they could find them, supernumeraries were allocated. At Lowestoft, that was about 20 men per ship.
The English allocated 40 shot per gun, plus some special types for the medium and small guns. At the Four Days Battle, they actually carried 50 shot per gun.
With respect to ballast, very few ships carried iron ballast, due to the expense. For example, the galley-frigates carried iron ballast, as well as other ships "built for speed". The other ships usually carried coal or shingle ballast (the Dutch were reduced to using sand, which is very problematic, when it gets wet). Some examples of ballast carried are: the Royal Katherine, 145 tons; the Prince of 1670, 206 tons; and the Lennox of 1678, 325 tons. Frank says that the latter was required due to the increase in height of gunports above the water. Unballasted, the ships had a high center of gravity, which had to be compensated by increased ballast.