There is no way in general to paste without using the System Clipboard.
There is no way to restore the clipboard without issues. Regardless of the length of the pause after simulating the ⌘V, either the pause is sometimes too short and the clipboard is restored before the paste happens (and so the wrong thing is pasted) or the pause is sometimes so long that the user has a chance to copy something else which is then overwritten by the restored clipboard.
The Paste action, and Type a Keystroke: ⌘V are pretty much functionally equivalent (the only difference is the delay after simulating the keystroke that Keyboard Maestro waits until it progresses - one uses the Copy/Paste delay, one uses the Simulate Command Keystroke delay).
The Copy action is different to just a Type a Keystroke: ⌘C in that it actually waits for the clipboard to change.
So, except in rare cases, do not restore the clipboard and use the Clipboard History as necessary, or restore the clipboard and either ensure you manually stop yourself long enough for things to happen, or accept the loss of robustness.