Definitely read the trust doc. The trust likely became irrevocable at death and should have filed 1041 each year, but since there was no income or expenses all those years one wasn't necessary. (Expect IRS to come back when the current 1041 is filed and demand the past ones--a simple letter should clear it up.)
What you are finding on the tax return makes no sense. If you brought the gain to zero, then line 9 (total income) should be zero. The tax on nothing is nothing. Further, if you marked the box for final return, all income and expenses get passed through to the beneficiaries and the trust pays no tax. Perhaps you haven't added the beneficiary info yet so the program doesn't know what to do with the income distribution deduction?
Realtor fees and closing costs get added to basis. (They can't be treated as administrative expenses because a "related party" was living in the home.) Fix up costs are also added to basis. Your fee, by the way, is deductible on line 14, even if it hasn't been paid yet or goes into the next fiscal year. I don't have the cite with me, but politicians (many of whom are attorneys) decided unpaid attorney fees could be deducted and for some reason included accountants in on the perk.
Property taxes usually go on line 11. However, if they were paid on behalf of a beneficiary who was using the home, you can't deduct them. They instead get taken from that person's share of the distribution. You really need to read the trust doc to determine what to do.
Don't be afraid of this. It's a very straightforward 1041--one transaction and some expenses. The 1041 instructions are all you need to read.