Use Delay Start [4.0.0.0;5.9.9.9]. That rule template can be configured to trigger at runlevel 40 and disable this rule. Then it triggers again at runlevel 100 and sets a timer to wait an additional configurable amount of time before reenabling the rule.
I use this to keep some sensor readings from pounding on a rule all at once when the Things start to come online. I wait about a minute after runlevel 100 and on my system that works great. You’ll have to experiment to determine the ideal amount of time after runlevel 100.
If runlevel 100 isn’t reliable on your system you should look into why and fix that. But in the mean time you can change the rule triggers to 80 or 70 or whatever works best for you.