There are mulitple issues that can be causing your hydro problems.
1. Did you test the old hydro pump? Was it bad?
2. Properly clean and flush the system?
3. Did you properly prime the new pump?
The charging issue. First measure voltage at the battery with engine off. Next measure voltage at battery with engine started running at curb idle. Next rev engine to high idle measure voltage again. Then let engine run at high idle for ten minuets and measure voltage again. With these reading I can better help you diagnose your problem.