You are exactly right. That's the problem. "Hard" money is money contributed directly to a candidate. If you run an ad like what you describe, under this bill, it will be considered a contribution to a candidate. That means the ad falls under the contribution limits for hard money. If your ad costs more than those limits, both you and the candidate broke the law.
If you run an ad prior to the 60 day cut off, it will be considered a direct contribution or "Hard" money if you had contact with the candidate. If your ad costs more than the limit you and the candidate are committing a crime.
So if LULAC sends Pat Buchanan and whoever is running against him a questionnaire, and they answer, then LULAC runs ads saying that Pat is a racist because he is against flooding the country with criminal aliens, the ad would be counted as a hard money contribution to Pat's opponent. LULAC and Pat's opponent would be subject to all the limits, disclosure, etc as if they gave that money directly to the opponent. If the ad costs more than the limit the candidate and LULAC have broken the law.
This is why everyone from the ACLU to the GOA is against this bill. It is a direct attack on the First Amendment. The Supreme Court already ruled that the Congress cannot limit spending so now they are going to call spending contributions. It's like Bill Clinton saying oral sex isn't sex.
What's the difference between spending and contributing? There is none.