I at least go through one motor every winter. I don't do anything real special for cleanlyness. I do put paper down on the benches, and cover everything overnight. I also make sure I do a decent cleaning of the shop before getting started...and no sweeping during the build, as that lifts a lot into the air. If in doubt, clean it before you put it together. I think some guys go overboard with the clean deal. No, you don't want dirt or metals in the fresh engine. But dust in light amounts affects nothing. I have never had any contaminant failures in my 8000 rpm small block, and I run an reuse everything just about forever because of my budget.
You do have to watch it when you are filing rings. That can be trouble if you aren't careful. Watch your clothing especially since you can drag filings over to the cylinders when you are fitting. If I do any porting, cleanup is better with a vacuum often times as long as you have a decent filter. Temperature can be important for sure. My old shop was not always heated, and my bearing measurements could change when the place heated up to room temperature. Just something to be aware of. I have always wanted to set up a nice engine building area, but for the one or two I do a year, it just isn't worth it. If I start picking up work from others, I will spend some time making the area professional. Having clean work bench area enough to set something down at any time is nice too.