The IQ Panel 5 has its own battery. If you replace the TAKE-345 modules with an IQ Hardwire Takeover, you can reuse the battery. How old is the battery? If it is close to 5 years, I would recommend replacing it.
The TaKe-345 is not compatible on the compatibility list for the IQ Panel 5 however it could still work with it. Since it is not on the list, I would recommend you replace it with a PowerG takeover module and a zone expander to be able to reuse all 16 of your hardwired zones.
It sounds like there may be an alignment issue or a weak magnet if it chimes when opening/closing but shows open when closed. Make sure the magnet and the sensor are aligned correctly on the window or frame. Use something metal to check the magnet strength. If there is a bigger gap between them, the issue could be that the magnet is not strong enough.
It looks like you would need one IQ Panel 5, Your additional secondary keypads, One hardwire translator and one zone expander for your hardwired devices.