I would agree that IF there is nothing special to do regarding the pumps (i.e. if you don't have to make the controller turn on a pump) then everything is relatively strait forward.
The most difficult parts would likely be replacing the valves and burying the wire.
On the subject of backflow...
Because this is a manual system, it sounds like most people here are placing their bets that there is NOT a backflow installed. If there is, then you would find something like one of these(http://www.sprinklerwarehouse.com/Custom/tscatlist.asp?PID=231) somewhere between the valves and where the system ties in between the two pumps.
A Pressure vacuum Breaker (PVB) should be installed above ground level and 6-12" above the highest head. A Reduced Pressure Assembly (RPZ) should be installed above ground (but perhaps hidden in a box). Its height relative to the heads is irrelevant. A Double Check Assembly (DC) could be installed anywhere it's accessible for testing and maintenance. The last option would be anti-siphon valves, but the valves would have to be installed 6-12" above the highest head similar to the PVB.
If you do have to install an backflow preventer, the PVB is the cheapest, but has the issue of must be higher than the highest sprinker head. The RPZ is the most expensive and considered the safest, suitable even if you inject fertilizer into the irrigation system (fertigation), but is has to be installed above ground. A DC is the easiest to install because it can be located anywhere (indoors or out, above or below grade), but it is considered the least safe and generally unsuitable if anything is being injected into the irrigation lines.
Additionally, you need to check with local building codes. They vary widely around the country. Some places are so flexable that they simply ask that you install something... anything... for backflow prevention. Some places are so strengent that they require part number XYZ be installed and that it has to be installed by a certified plumber.
