Are you sure the pump is in modulating mode ? It doesn't sound right that it is still at "100%" (how are you determining that ?) when most of the radiators have closed. You shouldn't get a lot of noise when most of the radiators have closed because a modulating pump should sense the restriction and reduce the flow - in fact most will reduce the pressure when they sense restriction, versus a fixed speed pump where pressure goes up as the system gets more restricted.
Is the pump built into and supplied with the boiler or is it externally fitted ? What model of pump is it ? Most modern modulating pumps can be put either in a fixed speed mode or modulating mode, so I would check that it is not in fixed speed mode.
I have a Grundfos UPS2 15-50/60, it has three fixed speeds and also three modulating speeds. I'm not able to use the modulating mode on my system as most of my radiators are microbore so it senses a high restriction even with all radiators open and slows right down to a flow that is insufficient. (My boiler needs a minimum flow anyway so I can't use modulating mode for that reason)
There is some debate about whether you should balance radiators to give a specific temperature drop between supply and return pipe (typically 11-20 degrees) or whether you should balance them to cause all radiators to heat up at an equal rate with all radiators full on from a completely cold system start.
Most information you'll find online seems to give the temperature drop method, but I'm squarely in the latter camp - balancing is to prevent radiators with "easy" flow paths stealing all the flow from those that are further away or have more restricted flow paths. A balanced system is one where all radiators heat up at about the same rate from a cold start with all radiators turned fully on. (On the TRV side only obviously) This can be easily checked by running around the house with an IR gun measuring the average panel temperature during that warmup phase. Keep going from radiator to radiator measuring the temperature as they warm up, looking for ones that warm up before all the others, or for stragglers that seem to be struggling.
You can also measure the difference in temperature between the bottom left and bottom right corners of the panel to get a fairly good idea of the temperature drop across the radiator (not as accurate as a clamp on sensor on the pipes but good enough, and very quick) however what you will find is that if you have a mixture of radiator sizes and types that adjusting them all to get an equal temperature drop will not give you a balanced system and as you have found, sometimes its impossible to get the oft stated temperature drop without almost completely closing the valve. (Then it takes forever for this radiator to heat up as it is hardly flowing)
This is particularly the case on a narrow radiator or one that is not a finned convector - a small non convector simply can't loose enough heat at normal flow rates to get an 11 degree differential across the radiator, unless you restrict the flow down to a ridiculously small flow. On the other hand a big 2 metre long 600mm high dual skin convector may have more than 11 degree drop even with the lock shield valve right open - as it is so good at loosing heat to the room.
Personally I would aim to get the temperature drop you are looking for only for the biggest radiators you have and accept that smaller radiators will not be able to achieve this drop, and don't have to. Then verify that warm up rates from a cold start are about equal on all radiators. If there are any radiators that start getting hot before all the others, those need restricting. Typically these would be ones close to the boiler. If there are any that are lagging behind the rest of the house leave those fully open and restrict all the other radiators in the house a bit further. I have one room on the far corner from the boiler with a 1.6m convector and even with the lock-shield fully open it is the slowest radiator in the house, so not much I can do there. It does get nice and hot but just takes a bit longer than the others.
If you can't get a sufficient temperature drop even across the large radiators without a ridiculously small lock-shield valve opening then your pump flow rate is too high - instead of trying to restrict all radiators to try to get around this its better to reduce the flow rate of the pump. If the largest radiators have too big a drop across them even with the lock-shield fully open you may need to increase the pump flow rate.
I've only balanced a couple of systems but it can be a very tedious time consuming process if you want to get it right, especially when you have to let the whole system fully cool to re-test the warm up rate from cold. Also if you restrict a lock-shield valve you have to wait a long time for the radiator to cool before you can confirm what your change actually did to the drop across the radiator. So there is lots of waiting and going around and around the radiators repeatedly.
If you don't have one, I'd recommend getting a cheap IR gun, this is the model I have:
http://www.ebay.co.uk/itm/Digital-IR...YAAOSwhDdXD1Pr
An IR gun will make the whole process much faster and easier.