good luck! Can't wait to see the new setup!
And I'd agree, the best plan would probably be to pull the plants first, then let the filter do it's thing for a little while so you can see who's still in there.
As for keeping the filter full of beneficial bacteria, if you plan to sterilize it to make sure it doesn't have any nematodes etc in it then you'll lose all your bacteria. If you plant to clean it well but not sterilize it, do it in tank water if you can, otherwise in fresh dechlorinated water. Then you'll have to keep the filter running on a bucket or something that has fish in it as an ammonia source. Or hook it back up on the tank as soon as you get the tank moved and then either put the guppies back in even if you don't get to planting, or add a little bit of food even if there are no fish/shrimp because the breaking down of the food will release some ammonia. The bacteria need an ammonia source to survive.
If you only have 2 surviving guppies and possibly some shrimp though, i'd personally go ahead and sterilize the filter and then shoot for a silent cycle in the tank, a pair of pygmy guppies and a couple shrimp aren't going to add a whole lot to the bioload, or if you have somewhere else to house them, you could do a fishless cycle. I find that as long as you stock slowly and have a beneficial bacteria seed source, silent cycles are pretty easy to achieve as long as you plant heavily. You may still need to do water changes if ammonia / nitrItes creep up at all, but when I did my 30 I found they eeked up to .25 over the course of a few days, and then I would do a water change, but the stems took care of the rest
