Can I still use polyiso to insulate a rim joist that is irregular?
I am about to jump into insulating rim joist in the my crawlspace, but as I am cutting pieces for it, I am starting to realize that foam often will not be 100% flush with wood and in some spots there will be resulting small cavity behind. Will that create a problem or is little bit of cavity behind fine, as long as I make sure all pieces of foam are foamed in just right?
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It's probably possible to install a bunch of very small rectangles, taking care to push each small rectangle tight to the material that you are trying to insulate, and then to seal all the small seams with canned spray foam.
But it is much easier to just go to your local lumberyard and buy a two-component spray foam kit. For more information on insulating rim joists with a two-component spray foam kit, see Basement Insulation — Part 2.
You may also want to read this article: Insulating Rim Joists.
However you decide to do this work, (a) You don't want to leave any air gaps between your insulation and the rim joist, and (b) It's important to seal all seams so that the work is airtight.
Considering it is ~50F in the crawlspace, are there any kits that can handle surface temperature like that or should I wait for summer?
If you store the 2-part kit in a warm place it'll still be warm enough to do a fair amount of sealing. You can heat up the surfaces you want it to bond to with a heat gun (or a hair-dryer) just prior to hitting it with the foam.
The cavity between the rigid foam and band joist is fine, but allowing basement air to convect into that cavity is not. When using the cut'n'cobble approach it's better to cut the rigid foam 1/2" shorter than the dimensions of the space your filling, leaving enough space around the edges to insert the flexible nozzle of a can-foam in far enough that you can leave the bead of foam on the band joist itself and let it expand into that gap, which makes for a fairly robust air seal.
Complicating matter is that the bricks you see in there were placed likely couple decades ago likely to meet the fire code. It looks like it was rushed - sloppy. I also think I have a balloon frame from crawlspace to 2nd floor (2nd floor was redone in 70s). So with zero insulation above, there is a straight shot up. Now that I think about it, it is possible for inside air, that leaked from 1st floor, to get to the cavity in the crawlspace.
I think I might be stuck with doing 2-part foam.
Touch N Foam has low temp polyurethane foam sealant I have used with a foam gun. I wonder if there is something little more colder surface tolerant. It is hard to keep the space properly ventilated doing spraying AND keeping the surface at temperature. Also concerned that even with I was using heat gun to preheat the surfaces, the foam would harden in the nozzle.