I can't answer your other questions either because it's been awhile since I played this or I don't have the modding knowledge, but I can answer this one.
EDIT: Every time I see this thread get bumped I get really excited hoping TET came back...
My apologies for causing unwarranted excitement, Maimonides. I have gotten a lot of modding ideas from the Test of Time.
The mega pirates are needed to keep things from totally deviating from the history. If not for them, Europeans would be able to reach Australia, etc. in the ancient age. By the time the Age of Exploration comes along, the mega pirates are weakened enough & you are strong enough to actually follow the history. TET found a great & fun way to keep exploration & overseas expansion from starting way too early. Ancient sea travel in the Med is dangerous, but still possible because the distance between safe ports isn't too great. The mega pirates keep the Greeks from sailing to South Africa in the ancient age, for example.
There are 43 Advances to be researched prior to the Industrial Age, assuming that all of them are researched prior to advancement. The minimum research time is 4 turns. If all of the techs are researched at the fastest possible rate, that would give reaching the Industrial Age in 172 turns. That is faster than possible, but allowing for tech trading, and pushing research as strongly as possible, along with say the Great Library, it should be possible to reach or get close to the Industrial Age within 195 turns. The remaining 350 turns of the game cover 1800 years. The game runs until 2050. Subtracting 1800 from 2050 leaves you getting to the Industrial Age about 250 AD. For Ocean exploration, you need Astronomy and either Navigation or Magnetism, so you can start doing serious exploration long before reaching the Industrial Age or well before the date of 250 AD.
Herodotus reports a Phoenician expedition that circumnavigated Africa circa 600 BC, set out by Pharaoh Necho, which I consider may have actually occurred. Pytheas of Massalia circumnavigated the island of Great Britain in the 4th century BC, and may also have reached what is variously viewed as Iceland, the Faroes Islands, or the southwestern coast of Norway. Wherever he went, it was to the north of Scotland. The Irish Christians, sometimes called the Westmen, reached Iceland sometime in the 9th Century AD, after the start of Viking raids on Ireland, being followed by the Vikings in the 10th Century, and the Westmen may have reached Greenland as well. Various Norse explorers, beginning with Erik the Red, reached Greenland, Baffin Island, Labrador, Newfoundland, and possibly penetrated Hudson Bay, all of this around 1000 AD.
In size and sailing characteristics, the Norse trading vessel, the Knorr (or Knarr), is quite comparable to the caravels of the later Portuguese and Spanish, and probably manned by far superior seaman. While the Phoenicians and Greeks might have had difficulties making it as far as the New World, they could have easily done much more in exploring Africa, and may have. If the Norse had pushed a bit harder, or been slightly more fortunate in where they attempted their first settlement, as opposed to a trade goods gathering expedition, which is what Leif Erikson's voyage was, they could have established a colony in southeastern Newfoundland 500 years before Columbus.
Pirate ships capable of stopping galleys from exploring the Atlantic, I can see that. Pirates ships making things difficult for caravels I can sort of see. Pirate ships capable of making mincemeat out of Galleons, Frigates, English Man-o-War, and Industrial Age Ironclads I take very strong exception too. Aside from giving the Iroquois, Aztecs, and Inca a free rein to expand in the Americas, there is no corresponding mass of ships in the North Pacific blocking Japan, China, and Korea. It is quite possible to travel from Japan, China, or Korea to North America entirely by Coast tiles, which can safely be traversed by any ship. That should be possible to achieve before even the Medieval Period is reached. If any of those Asian powers head for North America, there is absolutely nothing to stop them, and the Europeans may find when they arrive that the Aztecs and Iroquois are engaged in warfare with the Asiatics somewhere along the line of the Mississippi River or Rockies. Exactly how quasi-historical is that?
Based on all of that, the mega/super pirates are going to go. Making hash out of my galleys, I have been used to that since first playing the PTW scenario that came on the Civ3 Complete disks. Beating up on my caravels, such is life. However, when I have Frigates, Man-o-War, and Ironclads, then it is pay back time.