Kim,
You seem to be worried about the length of the radius rod, but if that isn't quite right, the engine should still run. The combination lever should ideally be at right angles to the valve centre line when the piston is at its centre of travel and the gear is in the mid position. This isn't essential though and some full size engines had vertical combination levers even though the cylinders were inclined. If your engine won't run in full gear you need to check the geometry of the gear. Is the return crank set correctly? Is the eccentric rod the right length. Any error here will put the valves out of phase and give them longer or shorter or skewed travel, but again, unless the error is gross then the engine will run.
I would suggest this. Block the driving axleboxes in the running position. Find the dead centres of both cylinders accurately. I assume you know how to do this but ask if you don't. With one of the cylinders on front or back dead centre wind the gear from full forward to full back gear. If the geometry of the return crank and eccentric rod are correct there should be no movement of the valve. Put the cylinder on the other dead centre and check again. There should be no movement of the valve. Do the same for the other side. If its not right then make an adjustable eccentric rod and use it to determine the correct length and make new eccentric rod(s). If the errors are small you might be able to lengthen or shorten them with the help of some heat and a bit of force as they did with full size locos, but it's not so easy with small ones.
Once you have it sorted remove the valves and find the distance between the exhaust edges of the ports. Check the exhaust edges of the valve heads are the same distance apart. Make sure the valve heads are all the same length. Correct any errors. Measure the distance of the exhaust edge of the port from the front of the valve chest. Replace the valves and with the gear set in in the mid position and the piston in its mid position (i.e. when the opposite side is at a dead centre) set the exhaust edge of the valve in line with the exhaust edge of the port. Do the same for the other side. Now see if it will run.
It should run in full gear without being lumpy. If it is check there are no tight spots. Usually these are associated with quatering, axlebox centres and rod length, but could be pistons fouling cylnder ends, or crossheads fouling slide bar ends.
Once you have it running and bedded in you can think about setting the valves with a little more finess, but the basic setting above should suffice to get you going.
Best of luck
Eddie