Tough questions Greg. In regards to how hard it is to install Soundtrax decoders, it depends on your soldering skills to a large degree. If you are comfortable soldering wires together you'll have no problem. What wire does what is pretty straightforward and well explained. Two leads (red and black) from the rails, two more (grey and orange) for the motor. two purple leads for the speaker. Other leads are there for lighting. The hardest part of a sound install is locating the speaker in the loco. I've only done steam, the tenders make speaker installation easy.
As far as what DCC system to use, well I guess they're all good. I use Digitrax. I think a Zephyr and a DT400 throttle is an excellant choice. I don't know much about MRC systems, as I recall at least one of their systems had trouble programming soundtrax decoders, it may have been an older one no longer available. You should certainly check before you buy. I think their are Yahoo forums for most of the DCC companies, I know there is one for Digitrax and Soundtrax. These are good places to check for how people are getting along with their systems. Just keep in mind that usually only people with problems post so it can be difficult to know how widespread a problem is.
If your track is glued down with insulators installed, just leave them and connect track feeds from each section to a two wire bus under the layout. Use 14 gauge wire for the bus. Say you use black and white wire (I strip the jacket off Romex cable and use that wire) Just connect all drops form the south rail(for example) to the black wire and all drops from north rail to the white wire. You can just leave the track power on while you connect each drop to the bus, if you cross the wires you will hear several beeps letting you know you have chosen the wrong bus wire. This works with Digitrax, the others must have short protection as well, might not have the beeps.
Good luck.