No acceleration, Will an alternator, not outputting enough amps cause this?

I wouldn't think so , scan for codes even if the light ain't on

Newer cars ARE very sensitive to voltage and amp output and can mess w modules and computer as there are a lot in newer fords, my wifes windstar is one of these. Surging is usually changes in fuel pressure so it is possible, but I would use an advanced scanner on it to see what the voltage is doing in real time cold and hot and loadtest to see whats going on. I would suggest cheapest first fuel filter first. And test fuel pressure.