I measure voltage = 4.85v on pin 1 of the IDE from a cold power on.
Warm reset: ctrl left amiga right amiga power light dims Voltage drops to 0.14v; release power light brightens voltage jumps to 5.77v; then falls back to settle at 4.85v.
With the TF I can boot to workbench from floppy and then access the HD - all partitions show.
It's unlikely that reset will be high immediately at power on as you'd be seeing a lot more issues. To measure this correctly you need to use a dual trace scope, trigger when the 5V supply rises, and use the second channel to measure the time until _RESET transitions from a low to high state. Which will typically be something like 200mSec, you won't see that with a multimeter.
In any case, the reset hardware sounds as though it's working normally, that's not the cause of your problems. It's going into run state after a warm boot, but there's somewhere else that it's hanging. You'd need to look further to see what's going on, which would be to see if the system is attempting to boot from ROM (_ROMEN going active), see if _OVERLAY (U350 pin 2) is getting set low, etc.
So it sounds as though the onboard IDE interface is actually working with the TF4060, but the issue is that it's either not accessing the IDE interface initially, or isn't correctly interpreting what it sees on the interface. Nothing in the U975, U976, U177 area is going to cause the problem you're describing. You can see if the IDE interface is being accessed by measuring if _IDE_CS1 (pin 37 of the IDE connector) becomes active (low) soon after power on. As with most signal measurements, you need to do this this with an oscilloscope as it'll only be a few milliseconds in duration.
It would also be worth sanity checking the operation of both those CPU boards in another A4000D just to be certain they do behave as expected.