Apple had a rotten day on Wednesday. After JMP Securities analyst Alex Gauna downgraded the company’s stock , Fortune points out, the stock fell twice as fast as the Dow at large. In dollar terms, Apple had its third-worst day on the market in its history. But it opened Thursday morning at $336.94, up from its $330.01 close.

Fortune’s Phillip Elmer-DeWitt has a thing or two to say about Gauna’s analysis — namely, that it was shallow and out of step with other analysts. Citing reports from Oppenheimer, Piper Jaffray and Credit Suisse that disagree with Gauna’s assessment, he closes his post by saying, “That, Mr. Gauna, is how real analysts do it.” Ouch.

Piper Jaffray’s Gene Munster said Thursday that while Apple’s supply line is likely to be affected through the June quarter, it shouldn’t hurt the company in the long run. In fact, Business Insider reported, Apple could benefit from its strategy to pre-buy and pre-pay for components, and Munster thinks current demand should “move shares higher.”

Apple’s supply line is showing wear in the shipping estimates for the iPad 2 on its online store. Those estimates now sit at 4 to 5 weeks.

A tipster told AppleInsider on Wednesday that the company may be reworking the way it handles launches. Reportedly, the company decided to send units to stores the night before its Tuesday shipment to improve inventory accuracy. That’s a departure from previous launches, where employees rushed to get devices on the shelves. There’s also been some talk about Apple’s new numbering system for orders. The company has switched to a randomized system, keeping everyone guessing about how many iPad 2 tablets have been sold.

Apple has yet to announce official sales for the iPad 2. Analyst estimates range from 500,000 to a million.

Also on Thursday, CNET reported that Toshiba’s flash memory complex located about 500 miles south of the Japanese earthquake’s epicenter is “operating as usual,” though the disaster could disrupt the supply lines for lithium-ion batteries.

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