Northwet I am fairly new here and in all my searching have not found a post saying to leave the covers on. For the OP and me what are advantages of leaving them on if you are not doing hard off roading.
Timing belt cover = plastic cover on front of engine? If this is the case removing this cover will make future maintenance much easier and give you access to water pump.
I'm not an expert but have read on here that aftermarket thermostats have smaller openings. My loyale runs about quarter way up on the gauge I think that's normal.