that seems to be a big issue with 1U cases and the fans
on the cpus are real short. Speed is a secondary issue.

no - the norm is not to put fans on the cpus at all, but rather
engineer decent airflow through the case and use substantial
passive heatsinks on the cpus.

I plan to put 4 standard size hard drives in the front of the
1U case. This pretty much blocks most of the airflow potential

nah. disks are 1", and 1U is 1.75". they also don't block the
whole width...

stable. Problem was that the cpu fan was about 3 inches
plus tall, way to tall for a 1U.

normal CPU fans are designed for desktop cases with crappy
airflow design. most of the air being so agressively circulated
past the fins is not fresh/cool air. the opposite is the norm
for 1U's, where the front of a rack is in the cold aisle and
thus taking in ~19C air, which runs straight through the node, and exits
to be cooled.