some steps can be combined, but I would
- convert rasters to the desired system of units (probably meters) while
- resampling the coarser rasters to match the finer rasters while
- ensuring that you specify a common extend while
- specifying a snap raster to ensure cell alignments
You didn't mention different projections... that is a tough call, but I would project to a common coordinate system in the desired planar units. There may be issues with maintaining a couple of the point above consistently.
In any event,
- always set and check your raster analysis and extent properties in the Environments tab within every tool that you use.
- Check the help topic for any tool you use at the very bottom and there is usually some specification as to the environments that are supported by that tool.
- Take your worst file, run the process and compare it to one that needs no work and if there are common spatial elements compare what happened to them during the process.
I probably have missed some and/or got a few out of order... again a few can be combined into one step.... if you aren't sure, do the steps individually. and... get coffee and make notes on paper
Addendum
The obvious... short paths, local data sources and destinations, no spaces, pay attention to dat type (ie avoid bit upscaling when possible, try a common nodata value when possible), In short... anything that will foul a result
