Oh yeah, you are the one with the cool new maf in an afm setup 
With that setup I'd consider adding a wideband, real-time air/fuel ratio gauge upstream of the cat(s) so that you can keep an eye on air fuel ratio and tune appropriately. When I've gotten into afm / fi tuning in the past air/fuel ratio has been essential to getting the tune and temperature management right. Being able to monitor/dial it in under loads/speeds were the more important points for tuning. If you aren't pretty dialed in you could easily be a bit more towards lean than the engine likes, and it doesn't tank much to cause heat to climb.
Once you get all of the monitoring in place it sounds like you'll be able to fine tune things as needed to get them just right. Beyond a/f ratio I also have had luck with temp monitoring at the head where you see temp shifts more quickly than via coolant/oil but still somewhat buffered compared to egts, etc.
I'd still tune the fan clutch but given the fi changes you've been making you could have more control over temps through a/f ratios and need to do more work there regardless of the cooling capacities.
Keep us posted.

With that setup I'd consider adding a wideband, real-time air/fuel ratio gauge upstream of the cat(s) so that you can keep an eye on air fuel ratio and tune appropriately. When I've gotten into afm / fi tuning in the past air/fuel ratio has been essential to getting the tune and temperature management right. Being able to monitor/dial it in under loads/speeds were the more important points for tuning. If you aren't pretty dialed in you could easily be a bit more towards lean than the engine likes, and it doesn't tank much to cause heat to climb.
Once you get all of the monitoring in place it sounds like you'll be able to fine tune things as needed to get them just right. Beyond a/f ratio I also have had luck with temp monitoring at the head where you see temp shifts more quickly than via coolant/oil but still somewhat buffered compared to egts, etc.
I'd still tune the fan clutch but given the fi changes you've been making you could have more control over temps through a/f ratios and need to do more work there regardless of the cooling capacities.
Keep us posted.