Recently had a situation where the furnace was shutting off the gas. It was found that the flame roll out safety was activating.
Originally I thought I had a cracked heat exchange, but on inspection it was not.
Ultimately I found that there was a bee's cone in the intake restricting the fresh air.
That has since been removed.
Now I am not getting a strong flame in all the tubes causing a roll out on the flames. Any suggestions on what to look for now?

How old is the furnace? The secondary heat exchanger may be the problem. On older units, the polypropylene lining can delaminate from the passages and block them. Go to furnaceclaims.com for more info.