The scout research team came back with a different name for the end user than the one on my Contract. For legal reasons

I'm not sure I totally understand the question. If this is in reference to your customer's business name - when in doubt, using the business name your customer used on their contract is likely a safe bet. If there's some minor difference (such as the inclusion of "Inc." or "LLC") it might not matter all that much. 

If you're saying that the project owner is different on your contract than what some research found, that can be a tough call. But, it's typically a good idea to be as accurate as possible. Relying on the project's Notice of Commencement for all entity names could be useful. Since the higher tiered parties are in charge of having that document filed, and since the notice's ultimate purpose is to inform potential lien claimants of the project information, it'd be hard to argue against using that information.

In either case, if you're unsure of what to do, including both names to cover all your bases could be another solution. Or, directly reaching out to the party in question to clear things up could be valuable. This would seem especially true in a situation where a lien waiver is being exchanged since the relationships on the job are likely OK and since the stakes are relatively low.