Lead-acid battery charging fixed current stage specification
Lead acid 36V would have 18 cells, assuming that 12V lead acid has 6 cells. 

Stage2:

The correct setting of the charge voltage limit is critical and ranges from 2.30V to 2.45V per cell. So 18 x 2.40 = 43,2V

Stage 3:

The recommended float voltage of most flooded lead acid batteries is 2.25V to 2.27V/cell., therefore 2.25 x 18 = 40.5V.

Source of the article


Based on recommendations you exceed all limits, but this recommendations are for common flooded lead acid battery. You should find what is the type of your battery: flooded, AGM, ...has additives: Calcium, Antimony,...

It is very possible that your voltage measuring method isn't very good. When you measure the open circuit voltage you get surface charge voltage, which can fool you. It would be necessary to load the battery with a known low resistance, for example 15 ohm and low Rdson MOSFET, for very short pulse duration and sample the voltage. 

You can improve your circuit with adding a series choke and freewheeling diode, if you wish to have almost DC current. Source