I'm a proficient user of my current Inventor software. I've been able to save the IPT file as an STL. However, S3D won't open it. Is it just too old to use for 3D printing?
Windows 10 has some new 3d tools if you have that. I've had luck opening STLs that wouldn't quite be right and resaving in 3d Builder (part of windows 10). Past that there is netfabb online that you can upload the STL to and try to repair.