Yes, it has RPM and PWM pins going to the motherboard and GND and 12V come from the molex.
Well that sounds like part of the problem. Try hooking the fans right into the mobo. I'm sure you have a reason why you have to split the rpm/pwm and power lines like you did, but the z87x-ud3h has 1amp per fan header, that's enough for 2x 120mm fans. I mean I'm sure you got a reason, but for debugging purposes, try to hook them straight into the mobo with all 4 lines to see what happens.
I mean just try the fans on different headers, then same header, gradually troubleshoot it. The mobo controls lines 1-3 as the same, so instead of splitting you can attach to one of those 3 headers.
I hooked up two more Vipers (for 4 total) through the splitter and now hooking the motherboard header up to sysfan 1 or 3 causes the fans to run full speed.
what exactly? 2 fans worked, then you got 2 more fans. What do you mean 'hooking the motherboard header up to sysfan1 or 3'. Hooking the fans to sysfan 1 or 3? I'm a bit confused.
So all I really want is for it to go back to how it was with the 2 fans hooked up, where they ran at half RPM all the time. It doesn't seem to be an issue with the splitter, since it works fine on the CPU header, so there must be something where it needs multiple fans hooked up or something? Maybe if I put one fan directly on sysfan 1 and then the splitter on sysfan 3 or something? I don't know. I have no idea why two fans worked fine independently, but one fan header hooked up doesn't work at all.
Then just run them at 7v. I hate PWM fans, a dedicated fan controller can be made for pennies using common electrical parts and soldering, or just using a fan controller for ~$20. But I mean if you just want half speed then just undervolt them or put a resistor on the line, seems pretty straightforward. The splitter is the issue, I assume. Can you not run the fans non-split and stuff to see what's causing the issue? IE try 3 fans, if that's good, try 4 on all different headers or whatever, good, then the splitter, etc...
Edit: It appears to be something with the splitter and the SYSFAN headers. It works as advertised on the CPU FAN header, but not on the SYSFAN ones, however the individual fans do work fine on the SYS FAN headers. So I don't know what would be different about those two headers, but that seems to be the issue. MAybe I'll just grab a couple of 2-1 splitters and see if they work any better.
CPU fan header and cpu OPT are linked and on a system, Sysfan 1-3 are all on the same control, and system fan 4 is 100% all the time 3pin. CPU fan can onlyl do pwm, while sysfans can do anything. opt can do anything too i believe.
You could also take the splitter out of the picture, run the fans like attached 3-pin fans. I've got a 3pin and PWM fan spliced together, I removed the sense and PWM line on the 4 pin fan and simply run it as a voltage fan off the motherboard on sys1, works fine to control it however I want with speedfan.