Dieter.koenig

Yeah, well, thats the main problem. Proprietary means that any standard fan is not guaranteed to even work properly. IIRC there are two types of issues with these server boards and standard fans. One is where you get errors since board doesn't recognize fan. The other is where its gonna run at 100% speed even if original had some sort of control going. You can probably solder any fan to have atleast 12V and GND, with yellow being possibly rpm/tach. But is blue PWM or something else, that I don't know.

PCIe 2.0 is the same as 3.0 but slower so a low end gpu like a 1650 doesn’t need the extra speed it will only make a difference on really high end graphics cards. When my gtx 1050 was on pcie 2.0 it didn’t make any difference going to 3.0.

no. only just recently the 2.0 bandwidth got saturated 
by a 2080ti. a 1650 or a super wont even come close the maximum bandwidth  of 2.0.

I've seen some guy said that "Most GPUs aren't even close to saturating pci-e gen 2 x16 speeds." on a post on this forum where a guy asked about using the GTX 1650 Super on PCIe 2.0 x16. And yeah I meant about the GPU (ASUS GTX 1650 4GB OC) one on my Server (HP ProLiant Ml110 G6) PCIe 2.0 x16 slot, it does also say the slot x16 supports 45W but I had an PNY Quadro 2000 version which it was 66.8 Watt and it worked just fine, so I guess the slot should produce even 75 Watt needed for that GPU and be working fine, if i'm right? (My server: https://support.hpe.com/hpesc/public/docDisplay?docId=emr_na-c01926955)

Did the laptop have switchable graphics back when everything works? If it doesnt then you could assume the iGPU is just disabled from the beginning, and currently the Radeon GPU is running fine only because the clock speeds are very low.

since you are in computer science, you will probably know more than be but if your motherboard has a monitor port on it, then you should be able to connect it that way on a very low settings and see if it will allow a system boot up so you can see what the issue code is, or start is safe mode. DDU the old drivers and reinstall them.
 
that is just my guess though.

well let me guess. you ordered used parts from Ebay, amazon and etc. from people who were not gigabyte, EVGA, msi etc. etc. right? those people are required to send it out but no time limit as to when they have to so best to avoid them. if you don't want to wait too long then order from one of the manufacturers like I listed above as they will usually send it out the next business day. 
 
take a look at these two links as they should help you pic a GPU that fits into what you are looking for.
 
 
 
sorry. I forgot to add that this first list only gives what the manufacturer of the card and what line it is like the Powercolor: Red Devil it doesn't mention that is a 5700XT card which is in the $500 range. so you will have to look up which one sounds good to you and then make sure it is the one you are looking at and want.