Could not find module 'MyCustomFramework' for target 'x86_64-apple-ios-simulator'; found: arm64, armv7-apple-ios, arm64-apple-ios, arm, armv7

This line is incorrect

cp -R "${SIMULATOR_SWIFT_MODULES_DIR}" "${UNIVERSAL_OUTPUTFOLDER}/${TARGET_NAME}.framework/Modules/${TARGET_NAME}.swiftmodule"

Should be

cp -R "${SIMULATOR_SWIFT_MODULES_DIR}" "${UNIVERSAL_OUTPUTFOLDER}/${TARGET_NAME}.framework/Modules/"

You'll need to check in the target folder

"${UNIVERSAL_OUTPUTFOLDER}/${TARGET_NAME}.framework/Modules/"

If there are files like

x86_64-apple-ios-simulator.swiftdocx86_64-apple-ios-simulator.swiftmodulex86_64.swiftdocx86_64.swiftmodule

Before Xcode 11, Apple seems neglect those files so your script works well.

From Xcode 11 those files are seem to be checked rigorously.

Swift 5.0-5.1, Xcode 11
Open Xcode, <your project>, Build Settings, Build Active Architecture Only and change to <NO> for Debug and Release. Architectures set/leave in Standard Architecture -$(ARCHS_STANDART), important is next step:
Valid Architecture: armv7, armv7s, amr64, amr64e, ADD here x86_64 and if you need add i386 for Debug and Release. (String: armv7, armv7s, amr64, amr64e, x86_64)

Choose any simulator in your simulator list and BUILT IT. DONE. 

I hope it is works for you.

Description of Architecture:

armv64: iPhoneX, iPhone 5s-8, iPad Air — iPad Pro

armv7 : iPhone3Gs-5c, iPad WIFI(4th gen)

armv6 : iPhone — iPhone3G

-the above if for real devices

i386 : 32-bit simulator

x86_64 : 64-bit simulator