Just my $.02 worth.
DME is made with a variety of grains and you don't know the make up of the recipe used to create the original wort. The safest bet with Extracts is to use Extra Light DME as it by color alone doesn't allow for much in the way of anything but base malt. Pilsen DME is made the same way. Amber and Dark may not give the results you want because you are also going to add some dark grains to get the appropriate color and roast.
So i looked up a handful of partial mash stout recipes and found that about half use Amber DME. None use bohemian or Munich malts. I'm gonna go with Amber as my base, but will swap the bohemian for something else, maybe Maris otter?
I agree with @RickBeer, you have already begun to cold crash the beer. Just finish and then bottle. To help everything out, maybe do your carbonation at a slightly lower volume (say 2.3 instead of 2.5) and then store them at 75 for 3 weeks. That will make a mini fermentation in the bottle and should clean up any yeast issues. Then store them in the low 60s for another 3 weeks prior to drinking.