Did you change the controller when you changed pumps? A TPH 050 controller will not run a TPH 060 pump.
50% indicates that you have a controller issue, not a turbopump issue. There is nothing in the pump itself that governs the speed of the pump - the governance is all in the controller. I would assume, based on what you've written, that you have a functional 050 pump and a malfunctioning 050 controller.
In order to properly run a 5970 you'll need somewhere around 40-80 milliTorr vacuum from your rough pump. On a '70, insufficient roughing looks just like a turbopump issue - without a foreline gauge it's really hard to tell the difference. You potentially have a leaking rough pump vacuum line (seen it before), or a leaking connection. Can you hear the rough pump gurgling? If so, you have a massive leak - check all your connections.
You don't want to plug the rough pump into the back of the MS - that is a fused connection that only provides enough power to run an old E2M1. You need to use at least an E2M2 or equivalent to get decent vacuum - if you're not doing this, change out your rough pump.
As HB3 points out, always troubleshoot a '70 without a column installed - butt plug the transfer line. Also, if it's been stored, tighten down the transfer line nut - it uses a metals seat and over time they loosen. You can get replacement seats from SIS.
The '70 is a great box - we run 5 of them. Once you get the vacuum solved I think you'll be impressed.