How low did the fluid level in the transmission get? Did the pinhole in the cooler line dump out a significant amount of trans fluid? How many miles did you drive while it was leaking fluid?
Have you ever performed a transmission service and replaced both the sump filter and the cooler return filter? If not, check the part number on the cooler return filter. If the last two numbers are "AB" then it is time to get a new filter. The AB filters are suspect and can possibly allow trans fluid to drain back out of the converter and cause a delayed engagement.
I would also get a scan tool hooked up to this thing and see if there are any DTC's set. You might find one for loss of prime. If you decide to drop the pan to have a look, you can see if you have any debris in the pan.
Its also possible that you have an internal issue with the reverse clutches. Low gear requires the application of the low/reverse clutch and the reverse clutch. Since you have 1st gear then I suspect an issue with applying the reverse clutches. There could be an issue with the valve body, precisely the low/reverse switch valve, causing the loss of reverse.