GPU in 16x slot but GPU-Z reports running at x1 speed?

Wellllll what you have there is a mix of several things :

1 - For starters there are kits on commercial stores that can run 16x PCI GPUs and lay it to other interfaces through cables like NGFF or PCI-e interfaces at 1x bandwidth . According to its users they are able to receive high fps , little less than if the card was plugged in to board so declining in PCI bus may hinder performance but not as far as killing it .

2 - Aged hardware usually have 2 symptoms , blown/deteriorated capacitors , and oxidized conducting terminals , the late can be fixed with ease by applying un-oxidizing agents . But capacitors however are getting harder to replace and pose challenges to even professionals as they reached tiny sizes only jewelers can handle . The result of these however are instabilities and crashes .

3 - If you are not getting instabilities and crashes , and are running at slow bus there might be hardware / incompatibilities where you need to check if there are a legacy bios option that might lead to this .

4 - Having low fps on one game may require you to search if others with same hardware are having similar issues or not , youtube now is filled with several videos testing same game on different gpus and bench marking their performance you may start there .

5 - Sometimes you are lead astrayed , the bottleneck might be something entirely else , like for example the hard drive might be running super slow , or even having several services running that are locking the hard-drive and slowing whatever dedicated for gaming from read / write bandwidth so you need to check task manager see on idle if disk usage % is still high .

6 - Sata drivers often require updates , working with wrong version number of sata driver may hinder performance greatly so you need to see if you have the latest driver installed .