All of the GameCube releases (PAL, NTSC-J, NTSC-U) are at 60MHz, so NTSC. They would require some massive rewiring to get them to run on PAL systems. That is all on Nintendo though. I think the most recent version of OoT that will run on a PAL system is currently the PAL v1.1 cart release (AKA PAL rev. A). No version of Ocarina of Time since then has been made to run on a PAL system.
So even if you loaded up the original, unpatched PAL Master Quest rom would not run on a PAL system.
Thanks for your response :-)
I've done some testing and got some interesting results.
Using the ROM I have extracted from my GC-Disk, I have created three patched versions (GC2v1.0, GC2N64, Aroenai's) and tried them all on my N64 including the original release. All of them worked fine except for the issues I previously mentioned.
But since I have invested a lot of time and money into getting that far (buying a Retroblaster + the writer, buying a neat looking cartridge for OOT MQ, a Wii and the Master Quest Disk + softmodding said Wii and extracting + patching the GC game) I will not give up so easily on getting this thing to run on my PAL console :>
So after doing some research I stumbled across a post where somebody mentioned, that a PAL region N64 can output both, PAL50Hz and PAL60Hz, with the latter being generally poor supported. Long story short: Testing the ROM on my old TV yielded some interesting results. Although this did not fix the sound issues, I managed to get a clean and stable video output :-)
Now all that is left is to get rid of that annoying sound issue.
For reference, I have documented all of my issues on imgur. Sorry for the poor video quality. I had to use my phone as I do not have any capture equipment.
https://imgur.com/a/VP7TUtzAfter that, I followed the suggestion of Goemon, thank you dear sir

, and tried patching the game with PALadin. Unfortunatley though it did not change a single thing. But I've gotten some interesting info from the readme!
[ Some technical stuff ]
Usually the sound of a PAL'ed NTSC-rom is garbled - that's because
the soundroutine is optimized for 60Hz and creates soundbuffers
which are to small for 50Hz. This produces the anoying "clicks".
It's not possible to make a generic-fixing-routine for that. 
There are to many different sound-routines on the market.
(Of course all know routines could be build in...but that wouldn't
be a generic fix! - I also got to many false fixes when I tried it)
It's also _NOT_ a matter of sound-tables or something like that.
Changing the Videotable doesn't change the sound!! The changed
video-mode just isn't compatible with the used sound-settings
Hope this stops the whining about PALadin being unable to fix sound
and the requests for it in future versions 
There are Video-Fixes available which handle this problem.
But since this tool is from 1999 I could not as of yet find any informations regarding these supposed sound fixes :-/ Does anyone have an idea or a tip where I might have luck finding some informations?
Now for some interesting bits of informations I gathered while working on my ROM:
- Converting my ROM from n64 to z64 did not seem to be necessary. While the file extension is .n64, tool64 showed blue arrows pointing to the right and displayed the byte order as big endian
- The header of my original extracted rom red NZLP, but after applying one of the patches it changed to NZLE
- Changing the Header did not change anything at all (probably? Might have slowed down the sound a little bit)
- GCto1.0 and GCtoN64 both work emulated with project64, but Aroenai's does not (neither with AA nor without)
- Funfact: The creator of PALadin is a group called dextrose. Their homepaged redirects (
www.dextrose.com) to
https://krikzz.com/store/ 