I was in my pre-teens when I realised that this was something my parents did, not something I believed in. The 'personal relationship with Jehovah' idea rings a bell - I'd no idea what it was. Still don't really understand it. Does he talk back? I asked really honestly and was listening hard for a reply. But, yeah, not something which happened for me.
Was always a bit geekish and bookish though, and I was reading stuff which was dismantling the whole Abrahamic religion belief set through the historical evidence really. Would have been an even quicker process if the internet had existed - having to chase down the sources via interlibrary loan was a slow process! Wouldn't have really resolved the problem of being a minor stuck inside. Possibly would have given a better twist to how I did end up leaving, at least in terms of dealing with things afterwards.
Know that feeling described in the OP very well. Everything had to be questioned and tested again. Even more recently, it's been the past couple of years where I've properly dealt with some lingering niggles which were still there. I found it very disorientating as a late teen, especially with the shunning thing going on and coming out of a very sheltered life. Still find the whole thing rather curious and difficult to explain at times. Is what it is.