I didnt not flush it with any solvent however I did drain it as best I could and used an airhose to get some of the old oil out.
Dude! You have to shut down now - and thoroughly flush the ATF cooler section of the radiator.
Neglecting to flush the cooler (and check for proper flow rate) after a catastrophic transmission failure almost assures that the replacement unit will not last long at all.
If done right, a thorough transmission cooler flush is involved, time consuming, uses a lot of solvent/rags and is expensive. Unless you have a lot of time on your hands, it may be a good idea to just get a new radiator and be done with it.
Use the time saved to drop the pan and change the ATF and filter even if they were new when you installed the transmission.
Did you dump and flush the contaminated ATF that was left in the torque converter after the failure? It's too late now but, most of the ATF in the system is in the torque converter.
The filter was the right intention but there is a good chance that now, due to the amount of particulates remaining in the system, it is plugged. That also contributes to a low flow through the cooler. Take it out or change it.