The combined budgets of all of USU's colleges totaled less than $350M/yr as of fiscal year 2016/17.

https://www.usu.edu/budget/pdfs/factsfigures/2016-17%20budbook%20budget%20summaries.pdf

The combined budgets of all of the UoU's colleges as of fiscal year 2014 (latest available) was $1.1B of which the medical school alone comprised nearly $700M. Without the medical school it looks like the UofU would have an operating budget in the range of ~$400M with similar student size to BYU but with a richer mix of graduate students (even after excluding the MD program).

http://www.obia.utah.edu/budget/expenses/pdf/tablee4.pdf

The oft-quoted $3.5B budget number for the UoU is their consolidated expenditures including $636M for "public service" (medical clinics), nearly $1.25B for the hospital and another $550M for auxilaries.

http://www.obia.utah.edu/budget/expenses/pdf/tablee2.pdf

As a primarily undergraduate institution I would anticipate BYU's 2017 budget is in the range of ~$500-600M/year. I expect BYU's funding comes from:

Tuition/housing: ~$175M
Gifts/endowment income: ~$100-150M (operating costs of all university facilities are funded via endowment before they are built)
Research grants/contracts: ~$50-100M
Only profitable athletic program in the state: $0-15M

I expect the tithing funds contributed are comparable to but less than the amount the State of Utah contributes to the University of Utah (~$300M). I'd guess $200-250M/year, i.e. the ALUF's estimate missed by 3-5x.