First, welcome to EB! Second, that is a lot of Lego to inherit! Without building all of them or having the proper minifigs with the right set, it is VERY important to let bidders know that it is an "incomplete set". You should expect that, like everything else, a non-complete set will fetch less than a "100% complete". Mislabeled auctions tend to really anger collectors... finding new part, ordering other parts to even out shipping cost, extra shipping cost, etc ( a part could be 0.10 EUR, but cost 2.5EUR to ship). It's best to be as honest as you can, to avoid negative feedback. Some sets, like the Taj Mahal, could benefit from a few hours of your time to inventory.
As for different parts on a box vs. parts in the set: The previous owner may have switched or mixed them with another set. I know of no instances of a part being on the box and not included with the set. I'm pretty sure that all or most collectors, like myself, are after 100% complete sets or close to complete sets. If the sets are in pieces and you have no way to have a good idea of how complete the set is, it's best to state that. As a big buyer of used sets on eBay, I can get a good idea of how complete a small to medium sized set is, based on a few good, clear, pics of the set and/ or pieces. Instructions should also be noted as included or not. Same goes with the original set box.
Parts, it is possible to get replacement parts for the sets. The downside is the condition of the set condition vs. the condition of the piece(s). Lego are UV sensitive and will show that if they were not properly cared for. If certain sets have dull or "yellowed" pieces, mention that, along with the set completion info in the auction description.
Another option is to get a scale and weigh out bins, and sell them in lb lots or by set lots (numerous sets; 1 auction).
Finally, if this all too much, I make it easy for ya.. 50Eur + ship and I take it off your hands!
I kid, but I hope all that helps!