"apparently I must treat those loans as contributed capital."
Do you have money flowing both directions or only one?
I first read this as money loaned to the Sched C businesses, which of course, has no real tracking of Contributed Capital.
If there is money Out of the S Corp for "loans": Since loans between yourself and your own Sched C entity are not "real", their treatment in the S Corp should be treated either as loan to Shareholder or Distribution. You stated there are two shareholders, so two individuals getting K-1. That means Distributions would need to be 50-50, which normally is a problem when people take money like this. That's why the Loan to Shareholder is used, to offset inequitable distributions until this can be resolved. In this case, though, it seems you can offset the loan Out as distribution Out; just split it to the married couple.
For money Into an S Corp, you have to determine if this should be contributed capital or loan To the S Corp, and again, taking into consideration all shareholders. While the S Corp can have a Note Payable to the shareholder(s), I suspect you will be rebalancing all these mistaken values against each other. Until you come out at the end, it's hard to see what will happen with this part.
And you describe the land sale is both 2017 and 2018, so obviously, things are very wrong. The farmland never put in the name of the S Corp means it was never contributed to the S Corp.
"I don't even know how to appropriately remove the assets from the 1120-S, as "Removal of erroneous assets" as a description may not please the IRS. But its not a sale or disposition, the Scorp does not actually own the land its been reporting as an asset since at least 2013. Someone please help me as I have no idea what to do."
Can't you treat the farmland as Leased, and that means some values for asset and depreciation would be appropriate.
"Level Up" is a gaming function, not a real life function.