I have actually read this series over at Ad Astra but for some reason I don't think I ever reviewed there. I must say that you do a great job with your characters. Captan Sandhurst for example is impressive in the way he seems to just be an average officer of no particular note yet is on a road to being one of the great Starfleet Captains like Kirk or Pike. I especially like his trick in "Prophets and Loss" which is the kind of thing that James T. Kirk would pull off. Lar'ragos also has such a well detailed background while maybe being something of an anti-hero. He certainly contrast but also compliments Sandhurst. I also happen to like the mystery that is Lieutenant Juneau.
Another thing that am impressed with are the ground vehicles, combat equipment and special forces that you present in the series. It reminds me of the story "A Planet to Far" located here http://www.bettnet.com/startrek/index.html
for the well developed presentation of Star Trek ground warfare.
In contrast to the great characters and storytelling the one thing that has drawn my attention as odd is how weak you present the Gibraltar as being. The Constitution Refit ships have a warpcore that is a big as those carried by many 24th century starships so in being overhauled she could easily have been fitted with a modern core. That means that as far as power production goes Gibraltar should be a mach for ships like the Intrepid-Class for example which means she could support modern shield generators and phaser banks.
As for her warp speed the Constitution Refit was supposed to have a top speed of Warp 12 on the old scale which is a hair more than Warp 9.2 on the new scale. The toughest thing to bring up to standards would be building a new torpedo bay to replace the obsolete one she is equipped with. With the exception of that though I believe the Gibraltar while not having the range of a modern ship due to the likely lower fuel capacity should have the tactical speed, maneuverability and firepower of a modern mid size Federation starship.
Wow. Guess I gave that more thought than I had planed. Don't let that last paragraph get you down the series is great and I would look forward to seeing new adventurers of the Gibraltar and its crew. There are after all a number of points hanging unresolved and I believe their are a couple of unfinished stories in the series that I would look forward to seeing completed.