Texas lawyer here. Not giving you specific legal advice; I'm not your lawyer and you are not my client.
Just because you find it on the internet (including BP) does not mean it is right or even right for your situation. This statement includes this post. You can read the statutes directly from statutes.capitol.texas.gov (a place you CAN trust). Chapter 91: https://statutes.capitol.texas... and Chapter 92: https://statutes.capitol.texas...
Re: late fees - Side with Dad. Texas put in a safeharbor statute on late fees. See, Sec. 92.019(a-1): "For purposes of this section, a late fee is considered reasonable if:
(1) the late fee is not more than:
(A) 12 percent of the amount of rent for the rental period under the lease for a dwelling located in a structure that contains not more than four dwelling units; or
(B) 10 percent of the amount of rent for the rental period under the lease for a dwelling located in a structure that contains more than four dwelling units; or..."
Stick to that.
Re: LL attorney's fees - Side with Dad. If LL sues and looses, T should not pay LL's attorneys fees.
Re: utilities - Side with LL. That's however the roommates work it out. Not LL's concern to play ref.
Re: mold/walk through - Side with Dad. Don't bother with that clause, it is useless in my opinion. Can't make them agree to it if they don't have a chance to view ahead of signing. Give notice about mold - that it is everywhere. If mold shows up ***you*** should address it. Mold is typically indicator of water penetration.
Re: pest control - Side with Dad. LL responsible for providing habitable home. Termites are always, 100%, LL's responsibility. Rats: if b/c LL didn't seal holes in walls -> LL. Roaches: first time LL, if b/c way T lives (food left out, not disposed) -> T's responsibility. Wasps: T. Bees (swarming): LL <relocate don't kill>.
Re: adequate notice - No call. Many LL's get stupid on termination notice. Who really knows 60-90 days out? 30-days' should be adequate. Also, Texas puts on LLs a duty to mitigate losses and no double recovery. IDGAF what the lease says, you can't charge 2x or 3x as a "termination fee" and slide a new T in 5 days later that pays full rent. Go put that before a judge and jury of 6-12 people and see how well you look.