I usually fly .049-powered planes on 35' lines, up to 42' if I want slower lap times. 8-lb Spiderwire is sufficient; I have used 12#, depending on what is available when I go to buy a reel. Can't tell much (if any) difference in performance. My .061-powered models use 42' minimum line length, up to 52', again depending on the lap time I want. You have to be kinda masochistic to put an .061 on 35' lines, although I do it occasionally (too lazy to roll out another set of lines for maybe one flight).
You don't need to CA the knots if you use a Palomar knot, or two or three other kinds that are non-slip types. A standard double hard knot (square knot) will not hold in Spiderwire; it will slip out. (Unless CA'd I suppose!)
I don't have a TeeDee .049 so can't speak to the appropriate prop, but a 6x3 seems a little much, I would run that on an .061. My .049s (Norvel, VA, Black Widow, Brodak) mostly use 5" or smaller props, down to 4 1/4", x3" pitch. Whatever it takes to get the rpms up, the little engines don't lug well. The Cox black plastic 5x3 broad-blade prop is sort of my base, then I whittle down the diameter from there as needed. APC props perform better but will break, and will do more damage if you get a finger in one! I've found the APC 6x2 to be just about the ideal prop for an .061-powered stunter. APC makes a 5.5x2 that might work well on a good .049 for stunt.
Fuel, I've used everything from 10% to 35% nitro, castor oil and synthetic, it all seems to work pretty well--the higher nitro does I think result in easier starts. I don't habitually tach my engine runs, but I don't notice any real difference "by ear" in the various nitro levels.
You got pics of what you're flying?