Couple things.
1) I'd never do a lift kit... I bought a truck that had a levelling kit (makes the front sit as high as the back) and that was enough for me.. It changes the angle of all the front end steering/axles etc. That angle change wears everything a lot faster..
Do you really need the lift kit? I know they look cool, but if you don't need it, I'd take it off..
I take my trucks in some awful places, sand, mud, snow etc.. I've learned a good set of tires is much more valuable than a lift kit.. I usually put on a really good set of the biggest tires I can that don't rub or barely rub. And I've never had a problem going where I want to go. And to be honest, if theres a place I can't take my truck, I have no business trying lol.. I'll use the ATV instead.
2) I know everyone isn't in the same position as me and everyone is allowed to spend their money as they want, but I won't pay more than 25k for a truck. Obviouslty I buy used, but if you can find a way next time you need a vehicle, get something cheap and even better if you can afford to pay cash.. start putting 300-500$ away each month right now so when you need a vehcile, you can buy cash.
Back to your issue, as everyone has said your engine and lift kit are not connected problems.. I'm guessing the receptionist is confused.. She might have 2 customers quotes in her hand and didn't' realize they were not the same truck??? I'd call back and ask to speak to the mechanic or even stop by and speak to them face to face because your quoted issues make no sense.