A cliche can be good if it invokes a fond allusion. A cliche is bad when its just another overrused bit.
Don't worry about your inspiration as long as you keep your story-world consistant with itself. And never talk about your stigmatized inspirations - people who don't know manga will not recognize the references, but they will stigmatize it for the connection you established.
Of course, once you are repeatedly published, reverse that. Your love of manga will then spread to some of the people who admire your work.
There are some cliches that are expected - the good guy gets the girl, etc and its harder to make the story fulfilling if you dont meet that expectation.
There are some cliches that are just cliches. Having the cop whose about to retire, show his picture of the boat he just bought an hour before he is killed in action. Just stupid cliche. Avoid this in all instances except parody.