Bill,
Here is a picture of the oil fitting from a 1934 lightweight tank. I would think they would be the same as the 1935, though I note here both fittings share a common thread size where they screw into the tank. The standpipe for the return line could go into either hole, but is invariably situated in the one that places it within view of the oil fill cap, so that you can check the return of oil to verify the system is circulating lubricant.
If you get one of those tank sealing kits, they usually have a cleaning preparation included that helps etch out the rust. I like to slosh it around with some ceramic stones, the type they use in vibratory and tumbling tanks to deburr and polish machined and stamped metal parts. I like them better than small stones as they are more uniform in size and can be had in shapes other than 'pebbles' that have more square edges to scour the inside of the tank. They also weight less than stones, so are less likely to peen and dent the inside of the tank if you get carried away. Remember you should slosh the media around inside the tank, not shake it up like an aerosol can. The media can not scour the inside of the tank if it is flying through the air inside the tank, and all you end up doing is pelting the opposite wall and possibly denting it.
The 250 & 350cc were fitted with a toolbox within the right rear chainstay, but one can not tell from the catalog illustration if it is cast aluminum or sheet metal. It is a different shape from the 'standard' cast alloy toolbox Douglas was using from 1930 onwards on certain models. But that might be catalog artistic license. Either way, it almost certainly uses the Douglas standard practice of two single sided clips that clamp over the upper chainstay tube. The clips you describe with the square holes (for carriage bolts) sound like the correct items.
Yes the clutch will require a puller. If you can jar it off with a wooden mallet, then it is probably not a good enough fit on its taper to be used as is without some attention. Douglas were making some of these flywheels self-extracting. If you can find in the bits and pieces a thin threaded ring that fits the thread in the face of the flywheel (something like 1-7/8x20, if I recall correctly) then this is the flywheel jam nut. The idea is that besides jamming the flywheel nut, you can back it off a few turns, then when you back off the flywheel nut proper, the flange on it catches the jam nut and extracts the flywheel. It may need a few taps with a mallet to get it to pop loose if the taper is a really good fit (you should be so lucky.)
The alternate puller is to have (or borrow) one made from a bit of round bar threaded to fit the afore mentioned thread. These are tapped coaxial to take a fine thread bolt that pushes against the end of the crankshaft to extract the flywheel. Place something sacrificial between the jack screw and the end of the crank to protect the machined center in the end of the crank. A small coin will suffice. Again you may need to give it a tap to pop it loose; in this case with a steel hammer to the head of the jack screw, and not a soft mallet.
-Doug