If my Mother is staying with me right now, can she help pay for a new roof on my garage as part of her spend-down?

Swamp, your profile says that mom is in a NH, but your post reads mom is living with you & is doing a spend down.
Are there transfer penalty issue$ with mom already existing?

I think she can pay you a reasonable amount of room and board, which you could then spend any way you want, but you had better check first what is considered a reasonable amount and make sure you have proper legal contracts in place.
And you should be aware that you probably have to report that money as income.

Spend down needs to be for their care or their direct needs or their property.

It's your home, your garage, your responsibility to maintain.

No, I don't think so. That could be seen as a gift to you. I would talk to the Medicaid people before doing that.