The flame sensors need to see the flame, not to stay in contact with the flame, they need to see the flame all time, to adjust you can check the output signal and check for maximum reading, most sensors has a connector to inject clean air to maintain clean the flame sensor view. You can find...
I will recomend you to have a leveltrol transmitter from fisher governor or other brand, but the same measurement system, you can have water deposits at the upper side of your dp cell, even if you have filled with water this side.
What you need is a control system for a steam boiler, this systems operate with the measurement of the pressure of the steam, the water feed to the boiler, and the level at the drum, you can contact some Bailey Meters representative to show you what you need to control your boiler. If not I can...
I recomend you to use servo-operated level measurement, it can measures the interface with relative facility.
You can find this equipment at: http://www.endress.com.
You need to consider when you have emulsions oil-water that would dificult the level measurements
You don't need to sold the wires. What you need is to change the terminals from the termopar to the control panel, clean it and check for the wiring, if you have conduit pipes check if the wiring is in good condition and the insulation too.
I think you only need to put the proportional band adjust ad 100% and this give you the transmitter signal you need, you can vary that value it you need to fix another range of level.
Maybe your problem is the temperature at the top of the valve, and you need another material for the diaphragm that supports the temperature, you can check in a fisher governor catalog to find the material of the diaphragm you need
When the system is in standby and you don't have any problem the pressure should be at 100 psi, and by general it you have some fire the system need to increase the pressure some times to 300 psi it depends of the size of the equipment you want to protect.