| Hi gonzorob,
No matter how well an instrument is set up, the strings will buzz if you play them hard enough (unless your action is grotesquely high). So, unless you dig in that hard all the time, I wouldn't worry too much about the open E or A string buzzes.
In most cases, the intonation is the last thing you will want to adjust, as other adjustments to the setup will usually effect the intonation and you'll have to re-adjust it all over at the end.
To Answer your question: It does sound like you are ready to adjust the intonation. At the moment, I can't think of anything else you'd want to adjust first.
Usually, intonation adjustments don't really change or fix buzzes on a bass or guitar, but there are exceptions to every rule and every instrument is different, so you never know. Go for it and see what happens!
If you're interested in a guide to setting intonation, I just posted the steps on the thread "Bridge" originally posted by TylerDurden111. Also, in the "setup on a fretless" thread posted by ivyman, Jools4001 posted a similar reply on intonation.
Good luck. | 
