It is best to come out of the boiler with 1 1/2" or 1 1/4" black pipe directly into the pump flange. This makes a very secure mounting for the pump. Then come out of the pump with a 1" pump flange and 1" copper. The copper coming directly out of the cast iron pump flange eliminates the need for a dielectric union. There is no need for a shutoff on each side of the pump, as these pumps rarely fail when mounted in this position and the valves are often a source of leaks. If the pump needs to be changed, simply shut off the gate valve, the ball valves on the supply manifold, the feed water, and drain the boiler down with the boiler drain, you will lose less than a gallon of water.  You should not put any crossover pipes between the manifolds.  You should put a full flow ball valve on each zone. This allows a zone to be shut off in case of an emergency without shutting off the whole system. It is also easier to replace zone valves, and gives you the ability to meter or balance the system.
There is really no need to install temperature gauges in addition to the gauge that comes with the boiler. The temperature controls on the boiler are generally more accurate than most temperature gauges. If you do have a temperature problem you can simply feel the pipes to identify it. You can easily distinguish a 10 difference in temperature by feel.
   Flow meters are totally unnecessary in a residential heating system. Any balancing should be done by adjusting the return temperature in each zone, which can be done by touching the pipes. Every system should be designed with ball valves on every loop, to make balancing simple.
  You should come out of the boiler with 1 1/2" or 1 1/4" black steel pipe to help support the manifold.   
Be certain to use a boiler drain for this. Other valves will not tolerate the heat or pH of boiler water. The boiler drain at the bottom or low point of the boiler is not only for draining the system, but also gives you a point to bypass the fill valve for faster purging. You should always keep a hose adapter or washing machine hose for this.
ou should use an all brass fill valve. The cast iron fill valve is usually the first thing to fail on a hydronic system. When a fill valve fails it causes a low water situation in the boiler, which is a safety concern and does shorten the life of the boiler.
   If the fill valve is working properly the pressure on the boiler should be 12-15 lbs. when cold and 15-22 lbs.
when hot. A reading of 25# or more means that something is wrong and should be serviced.
   A ball valve should be installed in front of the fill valve, because they have a more positive shutoff. Also it is easy to tell at a glance that they are open or closed. Because there is a lot of oxygen in supply water these fittings should be copper or brass.
   This gate valve is used for purging and to service the zone valves and should be 1 1/2" or 1 1/4" to match the iron pipe coming out of the boiler. This is a good place to change to copper with a 1" brass reducing bushing.
   This should be a 1/2" boiler drain valve. It is the only purge valve you need. All  systems should be self purging, but this valve makes it faster and more positive.