I can tell you how the Pacbrake works on my 1995 with a 47RH Trans. (You have a 48RE) I also have an aftermarket Performance Transmission, the ATS Stage IV, but I used the exhaust brake before I got the ATS by using a Mystery Switch.
OK... When I was running a stock trans, I would be driving along and I'd need to slow down, and I'd throw the Mystery Switch which would force the TC Clutch to stay locked. Then I would just take my foot off the go-pedal and throw the E. B. Switch. Worked great, but I was always throwing switches and every once in a while I would forget to unlock the mystery switch while coming to a stop. The truck definitely didn't like that, and would buck and shudder while the stock TC clutch was locked but slipping--Ouch!--Not Good! But that's the way it was when I was running stock.
I got the ATS Stage IV trans and the TripleLok TC Commander and things are easier. Now I set my lock-up speed with a dial on the front of the Commander. I can set the Torque Converter to lock-up anywhere between about 18 mph on up to 55 or so. There is a steep, winding mountain road, which I have to descend about once every 2 weeks with no trailer. I put the Trans in 2 and I set Lock-up for about 20 MPH and I throw the Commander Switch. I do all this while stopped
at the Stop sign before I begin the descent. Then I take off. When I reach 19 or 20 MPH the TripleLok TC automatically locks up. Then, as I descend and take the curves, the Pacbrake automatically comes on every time I take my foot off the pedal and goes off every time I push the pedal down. Pretty neat. I put the Trans in 2 on this particular stretch of road, because it is so steep and winding, I know I won't need a higher gear. On a straight hill where I am intending to slow down from 70 to zero, I would be in D and I just keep the Commander set to 20 and keep the EB switch on and just let the trans shift down through the gears locked as the EB retards speed.
Now I am not sure if the 48RE can handle an exhaust brake without modifications like a Mystery Switch or not, but somebody here knows the answer to that. Hope this helps.