New Boiler and slight change to system installed in 2005

I have two questions about an in-floor Radiant system that was installed before I bought the place Cir 2005 or so. The home is about 4200Sq feet and was running a Buderus GB-142/45. The Boiler has been giving us problems off and on for the last 11 years. It has finally quit and I took the opportunity to try to update the system a bit.

as you can see the system was setup for a high temp primary loop with a injection pump to push into the secondary loop. as well as a system pump and a second system pump off the Tee to the boiler. I am trying to simplify the system and installed a hydraulic separator and just one system pump.

I already know (now) that I messed up the hydraulic separator since I reused the piping the hot side is currently coming into the bottom left in the primary loop and out the top left and the same for the secondary feed side for the hot is the bottom right and return top right. I did a test run and the heat is making its way over but not as well as before with the old system. Is that mostly because I need to swap both of the in and out from the primary and secondary loops? or did I also make a mistake by taking out the pump on the primary loop. The replacement boiler is a Rinnai I-Series 150,000 BTU Combi.

Any insight would be fantastic.