Your issue with the Romford wheels not fitting to the axles easily is not uncommon, if there's the tiniest burr or raised edge on the squares of either the wheel or axle. It's been discussed elsewhere; just a very light touch of a needle file usually sorts that out. Are the wheels running true, now that you've tightened up the axle nuts? I'm presuming that when you talk about there being a lot of movement, you're talking about side to side movement in the frames? If so, you'll need to fit spacer washers between the wheels and bearings to limit it.
Looking at the motor/gearbox assembly, you shouldn't have any 'balancing' problems which are often found with 0-4-4Ts, especially if you can get some more weight into the boiler at the front once everything else is assembled. Lead pieces secured with epoxy - not PVA - works for me. If you can tilt the motor/gearbox assembly up a little, that will minimise the amount of material you will have to cut from the boiler skirt. That's quite a large motor/flywheel assembly you're using, which is good for haulage, but does make installation a little more tricky. A light spring to press the bogie down gently, even if you have got the weight well forward on the rest of the model, will help with keeping it on the track properly when running bunker first. I've built a couple of these kits, as well as other 0-4-4Ts, including a Jidenco/Falcon Brass Kirtley 0-4-4T, and this has worked well for me.
Closing off the cutout for the original motor can be done once you have assembled the running plate and arranged how you are securing it to the frames. IIRC it's a slot arrangement at the rear, and one bolt at the front?
Keep going though - it's looking fine, and they do build up into nice models.
Mark