Hi There!
Wow! That's a lot of information in one post! I'll start in on the things I can answer (or provide a snappy reply to) and let others fill in the blanks.
1) MLX telephones are 2-pair digital units. You can use CAT-5 if you wish, but CAT-3 will work just as well. You can use either 568A or 568B wiring configurations (I always use "B") but make sure you stick with the same config from beginning to end.
2) MLX modules for the Merlin Legend feature individual jacks for each extension. If you have a group of extensions located in a general area, you could punch down the individual extensions to one side of the 66 block, run a 25-pair to some centralized location, punch the wires down to one side of another 66 block and run the cables to the individual extensions from there.
For POTs lines, modules feature 4-position jacks (think RJ-11X). While I prefer to run individual cables for each line, you could create a "snake" from a piece of 25-pair cable by crimping RJ-11 plugs on the side connecting to the modules and terminating the other side of the cables as required.
3) Voicemail is optional on AT&T/Lucent/Avaya systems. You would need to secure either a Merlin Legend Mail or an Avaya Merlin Messaging. These modules would take up 1 slot in a Legend carrier.
4) If I understand the question correctly, you can delay the auto attendant so calls can be answered by a human.
5) You can swap phones as long as they are within the same "family" (replace one MLX phone with another) You cannot swap phones between "families" without connecting to the appropriate module back in the controller (for example....remove an MLX phone and connect an ETR).
6) Unlike Nortel, Avaya does make various guides for AT&T/Lucent/Avaya systems available for the general public to view and/or download.
Now for a few of my observations......
The Merlin Legend has been off the market since 1999. It was replaced by the Merlin Magix which was produced up until April 2006 when Avaya retired the entire Merlin platform. The reason behind this is thought to be that the Magix would have competed directly with the newly launched IP Office platform.
Programming a Legend system will require patience and an understanding of Calling Groups, Overflow and how they inter-relate. The programming guides, while informative, are not exhaustive in how & how much information is presented. It really isn't something that can be learned overnight.
The R4 Merlin Magix does have a feature that will create a default configuration for voicemails & auto attendants if the voicemail is an Avaya Merlin Messaging R3 or R4 (A 2.5 might work but I'm not 100% sure). This will reduce (but certainly not eliminate) the amount of manual programming required for your configurations. The Legend does not offer that.
Also the Magix supports 4400 series digital telephones that require only 1 pair of wires per extension as opposed to the 2 pairs needed by the MLX.
The downside to the Magix is that hardware, even in used/refurbished condition, is still pricey.
Depending on the needs of your customer, would an Avaya Partner ACS be a better fit? The programming is much simpler; hardware is much less expensive and is still in production.