Mizzou,
First, your original issue.
Try this:
Stop your pump. Then close both suction lines by shutting off the ball valves.
7:10AM CDT...Mizzou, I forgot a very important line last night...you need to close your pressure side valves at this point as well. In other words all pipes to and from the filter (except backwash) are valved closed. Sorry, I forgot this
Next, remove the strainer basket lid. (it might be a little tight...it'll still have a momentary vacuum on it. If you're plumbed like I am, the strainer basket lid should come off but the water shouldn't drain out of the pump.
Remove the basket and clean it. Replace basket and the lid.
Now with the lid back correctly in place, you should be able to open all valves and still retain water in the basket.
Your prime should be almost immediate since the little air that has come into the system is quickly removed from the basket.
Let us know if that works. If not, tell us what happened, I may have another thought. Long primes are very annoying and not beneficial to your pump.
Secondly:
Ouch!!, I wouldn't do that. That can't be good for the multi-port valve. I don't think you'll lose prime if you shut off the pump first...and I was told not to shut off the pump when turning it to backwash so I wouldn't have to prime it again.

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To aid in the priming of a set up like the one described, close the MD line shove a garden hose (wrapped with a rag - to make a better seal) into the suction port in the skimmer. This will take 2 people; 1 to hold the rag wrapped hose in the line, and the other to start the pump when the water arrives. Then you can open the MD valve slightly until the air is out of the line- this should save you a few minutes. * Trying to do this w/ only 1 person may result in a rag becoming lodged in the skimmer line 

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