Are there any stored CEL (check engine light) codes? If you don't have a code reader, most automotive parts stores or repair centers will read them for free.
One has to ask themselves why the vacuumn hoses were removed and plugged; I suspect a previous owner was simply too cheap to buy some replacement hose, so they got capped off. Now the ECU/PCM is missing some input or getting readings from various sensors that are causing it to set adjustments to the fuel pressure to the injectors, and this could be why the engine is running rough.
Like you plan to do, replace all the lines, remove the batteries ground, wait 15 minutes, then replace (clears the memory) then start the engine and see if you got any improvement.