I think you will want to leave the valves in; you don't want any flow through there.
Re: Ign: Dunno about your engine but I don't think mine would notice two are offline. If there is an ignition indexed in some way to #1, then I'd have to disable 2 and 3, for the easy way out.
Re: Injectors: Perhaps short them out, or measure an injector and stick the appropriate resistor across there.
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