I'll call HR first

The reference about your English ability is not likely to be a problem. They already have first hand experience about you English ability. People generally look for other insights from references. Typically, companies only check references for the person they want to hire to make sure that there is no serious problem in prior jobs. Generally they don't score a candidate based on references.

It's very typical for a candidate to learn his status once in a while. I'll call HR first, and if they don't know, I'll talk to the hiring manager. I won't raise English as an issue. Once you raise it as an issue, it becomes an issue. Instead, just tell them you are really interested in the opportunity. Show enthusiasm. If you suspect that they worry about your English ability, just talk fluently.

Things may be brghter than you think.