5mm, is less than 1/4". The amount you can raise the seat to compensate for the new shorter crank is 1/2(!!) of that 5mm. I don't know... I just don't think the new crank length is contributing to your issues with the new bike. Can we have some details please? Frame size? Sloping, not sloping top tube? What shoes do you wear on the bike? When I bought a slightly too big road racer I found that in cycling shoes I could stand over it with zero clearance. Zero clearance is really all you need. It's negative clearance that causes... potential problems. But most people don't worry all that much about the vertical issues of a too big bike. The seat height adjustment is usually well able to take care of that. The fore-aft reach of a big bike is what literally gives cyclists a pain in the neck. You aren't saying anything about that. So... hoping to get more information before suggesting any other options. FWIW.