A couple of points:
1) For a relative scale, my BattleMoons are 10,000 KT.
This gives an EPM of 200 for P&N. Since your thrust scale is half of mine, a 10,000 KT ship in your mod would have 100 EPM.
At that rate, your Battlemoons would be able to go 2 or 3 sectors per turn (3 with propulsion experts).
You may want to increase the size further in order to slow them down without bending your laws of physics
2) Adding a large price to the hull of your BattleMoons can help immensely in balancing the tech. Be sure to test their combat effectiveness against standard ships.
3) Mammoth engines are very nice and useful for Human players, but they will FUBAR any and all AI designs. If you intended to make this a humans-only mod, ignore this.
4) You do not need to place any artificial restrictions on the number of engines. If a player accidentally goes over the 255 limit, SE4 will RCE, but will continue running. The player can remove the offending engine and continue play normally.