Today I went to the electronic market in Shenzhen and managed to get those IC's. A kind Chinese helped me to burn the original Commodore U901/902 GAL files on those 2 IC's for free. Back home I replaced them and bingooo...
Everything works like a charm now!
I am able to boot with cache enabled using 68040. I also got a new ATX PSU and checked, but there are no differences. I can still use the original Amiga PSU.
I have re-partitioned the harddisk, formatted and re-installed Workbench 3.1.4. After placing the 68040.library in the libs: folder I can boot from hard disk with cache enabled instantly. MuTools was not required to install (but I will install it anyway).
Conclusion: the problem were the PIO2 IC's U901/902 which the previous owner installed on the mainboard. These are working fine with the original 68030 CPU, but becomes problematic with caches when using a 68040 CPU. (Compatibility issues) The solution is to put the original Commodore U901/902 back and the problems are gone.