yusuf_prasajo, were you using Crafty inside Chessmaster? A lot of GUIs have trouble with Winboard engines like Crafty, so you might want to try using WinBoardX 7 or Winboard 4.4.1 as your GUI. You probably won't see as many time outs with one of these GUIs.
I used the Crafty 19.19 engine inside Junior 10 interface. I usually use Junior 10 engine or Fritz 5.32 engine, but mostly Junior 10. For analysis I think Junior 10 is more useful. For playing I also prefer Junior 10 but set up at at least 2200. This way the engine creates "small mistakes" (I think it is the best move within a short period of calculation) that is tolerable. And the point is how to beat the engine for making those small mistakes.
It seems like those small mistakes are actually the best moves that the engine can find within certain constraints such as calculation depth or number of iteration in the calculation algorithm. I think this is more tolerable than dropping pieces.
There's quite a few famous endgame philidor positions/techniques.
Yeah, he did a number of endgame studies. I think the basic winning position and technique for R+B vs R is his too.