Bill J,
I'm thinking about two things
1.) The stardate system: Do you have any idea about a logical system for this? The best idea I have is to have each week be one whole number on the stardate system. If you start with 1300 something like "Where No Man Has Gone Before", you'd have the system start in 2239; if you backtrack from the end of Star Trek TOS, you'd be around 5900 something and that would put the start of the system around 2156 which was around the time the Daedalus-Class was built IIRC
2.) Hull Designation and Ship Class: I'm thinking of going back to Matt Jeffries original idea of having the first digits indicating the number of class of ship built and the last numbers indicating the number of ships built in the class.
Matt Jeffries original idea had some flaws to it such as the fact that the NCC was based on the tail number of commercial aircraft (examples: N12345 - made-up number; N93119 - a 747-131 that blew up over Long Island in July 1996; N106US - An A-320 that crash landed in the Hudson in January 2009). Prior to 1951, commercial aircraft had an NC designation (ex: NC12345), and in the former Soviet Union "CCCC" was a designation used for commercial planes (and with Star Trek based around the premise of a World Government, Jeffries decided to combine the two resulting in NCC). The 17 designated the 17th class of cruiser built, and the 01 designated the first ship in the class (which would of course make the Enterprise, the Enterprise class which was later retroconned into the Constitution class after NCC-1700 was shown).
Since not all ships are cruisers -- there are destroyers, and frigates, and so forth, so I've decided to do the following
Prefix Letters
C = Commercial
X = Experimental
N = Starfleet Active
R = Reserve/Auxiliary Reserve
Suffix Letters (Type Designation)
KC = Dreadnought (Based loosely on the novel Dreadnought which had the dreadnought designated as MKC-2331)
CC = Cruiser (while Cruisers are generally designated CA, CG, and so forth, destroyers have DD as a designation rather than just D so there's a vague precident for it)
DD = Destroyer
FF = Frigate
SS = Scout Ship
As for the designations for Tugs (which for warp capable purposes would have to be basically flying mobile drydocks), Transports/Tankers I have no idea