I built the fuse as the planes say and had no trouble mounting my WREN and it does stay cool as is...but if you change that there should be no problem.
I ditched the speed brake as well and put in 2 large flaps as you suggest, these can be seen in my gallery (geh3) I operate mine with air cylinders
I also would never use nyrod in a jet, I buried 2 digital wing servos in my horizontal stab to work the elevators
I built the retract mounts except used thicker wood and lots of doublers, I have had no problems with them I wish there was room to put in longer legs or struts though
the plane is a blast to fly and always draws a crowd at my field
P.S I also built the wings as one piece since the plane easily fits into the back of my truck OK and I believe it is stronger that way!

good luck and hey,,, did you see the plans for the Eagle 7?