The 2 most common pumps recommended are the MCP655 and MCP355 (they are available under several brands).
The MCP355 comes with 3/8 barbs I think, however it is not speed variable, and is probably noisy (although there is a slower MCP350 variant which might be okay).
I have the MCP655, which is variable speed and can be made pretty quiet. It comes stock with 1/2" barbs, however you can buy an after-market top for it, which then allows whatever barbs you like.
I would strongly recommend you avoid kits. I have never heard anything good about them. One thing you need to be careful about is mixing aluminium and copper -- you will get galvanic corrosion (even if you use anti-freeze, although that will slow it down). And many kits use aluminium parts. Not sure about the kit you have specifically, but just a word of warning.
The only kits I would suggest, are basically just the normal bits grouped together by the vendor, like this:
Given a 'kit' like above (or a similar collection of parts), yes, fan speed control is fully available (assuming your motherboard can do it) via 3 pin plugs. Obviously some kind of fan controller can also help with this if your motherboard is deficient!
Flow rate is not really useful information, and typically flow meters of any kind add restriction (and hence reduce flow). The important information is really the heat of your components (ie CPU), which the motherboard/CPU usually provide anyway. If your flow stops, you will know about it!
Refilling is not something that should happen very often at all, assuming no leaks. However, bay res's are available if you want to be able to check the water level at a glance.
You can get something like the Typhoon III bay res, which mounts the pumps in the rear, however, I am not sure how well that will separate the pump noise from the case. I personally have my pump suspended with elastic to avoid it vibrating the case.
Most parts (pumps aside) have standard G1/4 thread connectors, which any barb size can then be screwed into, so you can keep the tube size consistent.
I personally use a silverstone CMD01 to monitor temps (both water and air), and I think it works extremely well. Can be picked up from amazon for $16 and you do not need an ESA motherboard to run it.
Hope this helps. Have a look at what is available at a retailer like I linked above (or sidewinders, both of which I have had excellent service from), and ask away.