I don't think there's a need to go above 740CC unless you're planning on making some serious power. After reading a lot and asking around here about alternatives, I would consider sticking with the Nismo 740CCs over JECs or other guys. Also, the tuners (SZ,etc) seem to have the 740CC base program nailed down well. Don't forget if you change to another type of injector you're going to need to get a new EEPROM for your ECU. Make sure to have the dual intake mod done at the same time to avoid needing another reflash.
http://z32.wikispaces.com/Fuel+Injector
Not sure why you would need to replace your valve covers. If they've never been done you can do your valve cover gaskets. The 2 intakes are rubber, but the 2 exhaust are RTV. FYI the exhaust covers are THE HUGEST PITA to get off/on, and get the heads cleaned up while the engine is in the car. I seriously wouldn't do that again unless mine were leaking. Also, another pro-tip about the exahust covers that isn't really mentioned in the guides. You'll need to get your EGR pipes out of the way. If you plan on keeping your EGR, this means unbolting them at the valve, which is going to be another HUGE PITA. Even if you're planning on doing an EGR delete without valve removal, its hard to get the pipes cut back far enough to clear the valve cover bolts.
Long story short, I would skip on doing exhaust valve covers unless its leaking or the engine is out. The intakes are very simple, and the ROI for them is probably well worth it.
Also:
http://z32.wikispaces.com/Valve+Cover
http://z32.wikispaces.com/EGR+Removal
http://z32.wikispaces.com/Coolant+Line+Bypass