Hi Jennifer,
We're also thinking about CLR but not yet ready, so I'm interested in your pain points since most likely we'll face them as well.
Here's my two cents:
For example 1: This is a big question around the approach (1st touch vs. all campaigns that touched the contact getting some %). There isn't a perfect answer but I guess that if you get too many complains with the 1st touch, you may need to change the attribution model. You shouldn't be able to adjust manually which campaign is the "main" - that's the magic that CLR will do for you. The key is to select the attribution model that everyone is relatively comfortable with, and NONE is perfect
For example 2: That campaign should not be marked as lead gen, and will count in CLR. In the settings > General > uncheck "Include in Opportunity ROI". That way, there shouldn't be opportunities tagged back to it.
Good luck!
Edited to add: As far as I understand the relationship for CLR is done by the email in the contact associated to the Opportunity (if you have Opps at a contact level) or the email for that contact belonging to a company that has the opp (if you have opportunities at a company level). So whatever adjustment you do in the campaign-opportunity relationship in SFDC, Eloqua will not care. To consider a contact "touched" by a campaign, you need to establish the response rules. By default, i presume something basic such as "opened an email" is not a response rule to match that contact as really "touched" by the campaign and hence, give some attribution to the opportunity. Could be attended an event, or filled a form, or whatever you have defined. So make sure you have those rules clear so you don't get more attribution that you actually deserve