5r55e Delay going into gear

[Jon94]

2006 Ranger 4.0 4x4 5r55e.

I just got the truck back from the body shop after almost 3 months of waiting for it to be fixed (see this thread for more on that: http://www.therangerstation.com/foru...hlight=crashed)
Now that I got it back, it behaves differently. When I put it into drive, it takes a full second to actually go into gear. Once it goes into gear, it shifts into every gear perfectly fine. The problem is ONLY when I first shift into drive. It doesn't do it when I shift into reverse. I checked fluid level and it's perfect.
I also noticed the tranny cooler gets really hot after a drive, way hotter than it used to. I remember coming home from work and feeling the cooler and it would be warm, but not very hot. Now I come home from work and the cooler is too hot to touch for more than a few seconds. I'm scared to drive my truck now. I don't want to damage it further. What should I do?

I should add the truck has only 34k miles on it. I did a pan drop and refill with Mercon V at around 25k miles. I also added a Magnefine filter at around the same time. I'm hoping the Magnefine is causing a restriction and is the cause of the problems. I'm going to remove it tonight and see if that changes anything.