Sian - E is doing what J did a few weeks ago. Fighting BT eventho he took great naps. Some days his naps were shorter and I tried to maintain BT, but in the end you know what happened. I transitioned him too soon and we were in a big mess. Now it has only been two days for us, but our nights have drastically improved. And we are doing the short am/long pm. I think you are going to have to do two things. One - cut one of your naps AND increase A time. I found that J needed both to go down easily and not have EWs.
On a 45min nap, J can do 4hrs and I witnessed this on Monday when I decided to give him two naps after a week of 1nap days. I even tried 3.5hrs and he fought, so I let it go and just spent more quiet time with him and in the end he fell asleep after 4hrs. Again, you know E better, but I know our lo's are similar. You could try just the 45min pm nap and see if he'll go down after 3.5hrs and if not, you'll know tomorrow that it should be 4hrs. I know it isn't ideal. Hope I have given you some insight.