Which one of those provisions violates the 1st Amendment?
Actually, 2 of them would definitely be...
They're state actions respecting an establishment of religion.
In that city,
if I cranked up the speakers and blasted Van Halen at 6am and 10pm, I'd get a ticket for a noise violation.
if I was slitting animal throats in my back yard without stunning the while they were still alive and conscience, I'd be getting hit with animal cruelty fines (and probably some sanitation violations)
However, they get an exemption to broadcast the Muslim call to prayer through loudspeakers at those times. That's religious favoritism.
As is the backyard ritual slaughter thing. If a neighbor complained and said "what are you doing, you've got a screaming convulsing goat bleeding out in your backyard, my kids saw that!!", I'd be getting arrested. However, they get a pass on it because it's "respecting a religious tradition"
As far as the Halal compliance on school lunches as a matter of funding and policy, if I was a city council member in any other city, and we decided to carve out extra funds for a more expensive version of school lunches for a secular reason (like tailoring it to our preferences, just cuz) we'd likely have some voters to answer to. However, if it was being done specifically for the benefit of one religion, that likely runs afoul of 1A.
That one is a case where "the reason matters".
For instance, if a city provisioned money to supplement school cafeterias to stock Coca-Cola products instead of PepsiCo products.
If their reason given was "Yeah, it's a little more expensive, but the Pepsi stuff wasn't selling, we were throwing a lot of it away, and the Kids prefer Coke", then that wouldn't be a violation.
However, if their reason was "Well, we're about 65% Baptist in this town, and PepsiCo did a Pride themed ad campaign we didn't like, so we don't mind using public money to make sure the school can buy from a different that didn't get into all that gay stuff to accommodate the Christians in town who want to have a different brand"
Then that rationale wouldn't pass the Lemon Test.
Changing laws, making exemptions to laws, and public funding allocation that is done explicitly for the purpose of accommodating one religious viewpoint cuts against the first amendment.