I've noticed a few differences between the DOS/DosBox version sold on GOG and the old PowerMac version:
-- The DOS version limits the number of Wagon Trains you can build; in the old Mac version (released, I believe, after the DOS/Win 3.1 game), you could construct as many Wagon Trains as you wanted. This means you'll likely have to build or buy Ships to hold all the Horses you'll need to fight the War of Independence.
-- Unfortunately, the DOS version prevents your Frigates from attacking Privateers from other nations without breaking peace treaties. Unless you're planning a sneak attack on another nation, this limits the value of Frigates largely to transport and attacking ships from nations with which you're at war. In the PowerMac edition, Frigates could attack Privateers with impunity -- in fact, this was the major reason for acquiring a Frigate.
Also, a few brief cautions on playing the game:
-- I seem to remember that there was a limit on the total number of units you could have -- I think it was 264 total. If you approach the limit, disband less valuable units like Criminals and Indentured Servants. I don't think the game warns you about the limit, but I understand that having more than 264 units interferes with the War of Independence by delaying the Royal Expeditionary Force.
-- NEVER leave a unit on a coastal square during the War of Independence. If a unit from the Royal Expeditionary Force attempts to land on that square, it will create an endless feedback loop that essentially destroys that particular game. Build a road network around your coastal colonies -- even on unused squares -- that will enable you to attack the REF without finishing a move on a coastal square.
-- NEVER assign a Colonist a task to a particular square that they cannot perform -- eg, assigning a Colonist to act as a Lumberjack on a Mountain square. If you do, the Colonist will disappear the next turn.

Strictly GOG version speaking here...

Wagon trains are limited by the number of colonies you have. Personally, I never needed more than a few as I use galleons for horse storage on the coastal cities. Related to this, you cannot create more than 11 trade routes. The 12th will break the game.

Am I mistaken here, I can attack all the pirates I want with any ship. They carry no flag. Admittedly I havent played in a few months. I may be thinking of pirate on pirate action...

There is a hard limit and I dont recall either, but I thought more than 264. Units will simply not be created when they should and you will loose all food/money used to create them. If you do run into it I would recommend disbanding cannons, ships, or wagons which also count toward the limit as they give no end points while even a lowly convict gives something. There is also a colony limit. 50 something overall which the other countries count toward. You can max out at 32ish without conquering other colonists.

You can remain on the coast, you should not block all spaces on the coast line. This will cause the REF to simply kill a unit to force a landing. The fix for the aforementioned coastal issue.

I dont recall ever seeing this even in the original version. In fact, I would recommend you do this all the time with tile labor due to the possibility of gaining that skill, especially the planters which can only be learned in the New World from tribal training. Perhaps this was a mac bug?

Re: pirate ships -- I'm playing the game now, and I've twice tried to attack Privateers with my Frigate, but each time I receive the warning that this will break a Peace Treaty. Could this be a bug? I have no trouble using my Privateers to attack other Privateers (or any other ships).
It's good to know that the number of Wagon Trains you can build is linked to the number of Colonies. And thanks for the caution about trade routes. I usually only set up a few trade routes during the game (mostly for transfering commodities and finished products) between two Colonies that are closely situated. I like having Wagon Trains available to handle particular tasks,
As far as having military units on coastal tiles, I posted the caution because of an experience I had playing the game on the Mac. In one game, during the War of Independence, an REF unit tried to land on a coastal tile that I occupied. The landing failed, and it created an endless loop in which the REF would return to the Mother Country and back to the New World without landing any troops.
This might indeed be a Mac bug. I found that I can build road networks around all my coastal Colonies that enable me to attack the REF without ever having one of my military units end a turn on a coastal tile. And usually by the War for Independence I've developed all the planters and other specialists I need.
Thanks for the tips. It sounds like you're experienced with the game. For me, Colonization is one of those games I keep coming back to -- its ability to create new worlds and the many options available for gameplay always offers a fresh challenge.