This is a bit tricky. I don't know the answer, but I can give you some facts and interpretations. You may want to consult an enrolled agent who is experienced in clergy matters, for a definite answer.
First, the premise concerns me, that you would have thousands of unspent dollars on your housing allowance. A housing allowance must be designated in advance and in writing by your church. It can't be changed retroactively, and it can only be changed going forward on a pro-rata basis. For example, suppose your church designated a housing allowance of $24,000 per year effective 1/1/18 ($2000 per month). On December 1, 2018, you asked them to increase it by $10,000 per year to cover the windows. That change has to be pro-rated, so your housing allowance for December could only be $2,833, for a total allowance in 2018 of $24,833.
The only way you could afford to cover the window work at the end of the year is if your original housing allowance was much bigger than your anticipated expenses, or you are trying to make an unallowable retroactive adjustment for 2018.
Second, there is the question of when the expense actually occurs. Does it occur when you sign the contract, or does it occur when the work is completed? There are arguments on both sides that I won't take the time to go into; in this case, I just don't know which is correct. If audited, you would have a reasonable argument to include the cost in your qualified housing expenses as of either date.
Third, is the question of whether you can deduct the amount that you borrowed as a single expense now (i.e. in 2018 or 2019) or must spread it out. I think you can deduct the amount as a lump sum -- if you have room under a properly constituted housing allowance -- because borrowing the money in your own name with a promise to repay is treated the same as paying the money directly in most tax situations.
However, you can only include the principal you borrowed as a qualified housing expense, not the interest you are forecast to pay; and in future years, you can only include the interest part of your loan payments as a qualified housing expense, and not the principal part of the payment.
