You are correct, there are so many options and possible configurations that it can be very confusing. Start reading the Virtual Private Networking faqs. They have the most detailed info out there on setting up networking under 98 over the net.
I used to do it quite often with a collegue down in Australia. We used vpn (not to difficult) and pure file shares (risky if you don't know what you are doing).
Are you familar with setting up a lan under 98? If so, it's not much more than a configuration issue.