I just started with JSNQ and I'm absolutely loving it so far. I actually need those big engines, tanks and multistage rockets now.
One Problem I have however is with some of the command Pods from Near Future. Specifically the ones with landing engines and/or RCS skirts (Mk 1 Nereid, Mk 3 Thetys and Mk3B Pandora). Parts of the pods are broader than the heat shield and I have been unable to perform a safe reentry with any of them even from LKO (much less from the Mun or Minmus). For now I'm sticking to pods that fit entirely behind their heat shield.
I would be grateful for tips on how to make them work. I usually aim for a reentry Pe of around 35-40 km to prevent my Crew from blacking out.