You could try taking the car to a dealer (call first) and see if they offer safety inspections. Some dealers will do this for free, where they go around the car and look for potential problem areas. Not sure if Honda does it, but most Volvo dealers will. Its a cheap way to promote service sales and it takes very little time for them. Some I've seen (a Chevy dealer, a Toyota dealer) charge a minor fee of $10 to $25. Or take it to the mechanic you trust if you have one.
Ask them if it feels rough to them. If you ask that at Honda, chances are you'll be asking someone who has been in many of these cars. If they say its normal, it probably is.
To be honest with you, and based on your description, it sounds normal. I've driven and ridden in quite a few Hondas over the years and all have had some kind of vibration, though its what I would call very faint on most. Even my new one (43xx miles now) has some at idle in neutral. It's more noticable when cold, but there's always a bit there regardless.
They're (Hondas) great cars, but they're not luxary cars. They're built to be dependable and practical first and foremost. A little vibration isn't a major concern with those features in mind. Even some high-end BMWs I've driven have had minor vibrations (though those were usually M models and most had an I-6 engine.)
BTW...if you really want to clean out the injection system, have it professionally done. The stuff you buy at the autoparts store is pretty lame compared to what most shops use. I know Sears does it for about $60 to $70 on most vehicles and I'm sure others are similarly priced.
