I've gotten the MKL 8M and the IDE68K stack to work on my A1000 some time ago, but I have since reworked the system with an HC533 which has both 8M and IDE, and a faster CPU solution, so I no longer have it the way you are trying for anymore. At the time it was a good system setup. I also had the Insider 1000 (1.5MB) on the CPU socket stack (had to customize the stack to support the height), so I had a 10MB A1000 (512K was Chip)
That said, here is what I recall from then:
I have a ROM Switcher module from Tuxbar86 (AmiBay) wired into the system that lets me pick Kickstart versions - I have 2.05 and 3.1.4. The 256K WCS upper RAM board is not part of the functional system as a result of the ROM adapter. I assume you have a simple ROM adapter replacement for the disk load of Kickstart, and want to use 3.1.4, and have similar mods done to disable the WCS.
The source for the signals the IDE68K uses I grabbed from the nearby VIA holes on the 86-pin edge connector. Use the schematics for an A500 edge for ref (for readability - all A1000 schematics are hand drawn and scanned, but the signals are the same, just harder to read) - Pin 1 is forward (vs rearward on an A500). Keep these 2 lines the IDE 68K needs as short as possible - A1000's can have timing tolerances that vary more than an A500 due to the discrete logic (vs GARY chip in the A500 absorbing most) and also that daughter board can pick up noise - it is popular to run a heavy ground wire from the PSU to all of the PALs' ground pins - Mine has it and I have seen many that also do.
You will need the 8M module in the stack because the A1000 only has 512K native. It plays a trick with AutoConfig in the 68K socket, and may render an external sidecar AutoConfig unable to function, but that is the least of your issues. It doesn't affect the IDE68K as that module is detected as motherboard resources, and not an expansion board. 3.1.4 will boot up to CLU in 1MB RAM with a small HD partition defined, but by the time the OS loads everything for Workbench GUI AND the HD partitions have their needs met, 2MB is a realistic minimum value for a 2-4GB HD in the system.
With 2.05, 3.1, or 3.1.4 ROM in the system, the IDE68K acts like an A600 IDE port - scsi.device in ROM is able to detect the interface and maps it as a resource into the system, and can boot from it.
Use HDToolBox to set up the IDE media with the Install disk. You have to let it read in the disk media info first before going into the partition areas and defining partitions. Set up your first partition for ~500MB, and in advanced, use 4K block size (this is the recommended smallest multiple for all flash media use - FFS or other computer filesystems), and let the rest of the media's space be for now. Reboot on the Install disk and format the partition, using the quick option. Let the installer copy the files to the HD.
Once you get that stable, you can go back in to HDToolBox and add additional partitions, if you need them. Although you can go past 2GB sized partitions with 3.2.4, adding more partitions, and larger ones, consumes more memory. I get by with IDE Flash DOMs of 2-4GB on my systems (with IDE), usually 500MB boot, and a pair of 750MB or 1.75GB partitions.
Note that the IDE68K can't work on native 1.3 or 2.04, as the scsi.device IDE code is not present in then ROM or the soft load Kickstart.