Yeppie!
Correctly indexed, #1 cylinder will be TDC and both valves closed. Double check that both #4 valves are wide open and #4 is TDC.
BTW, The piston should be on TDC of the cylinder you are adjusting. If you will start with the #1 cylinder and make a mark on the front pulley with a whiteout pen etc and then a reference point to it on the block somewhere then make another mark on the pulley 180 degrees across. After you have adjusted the first #1 cylinder to get the next cylinder in the firing order to TDC turn the engine untill the next mark on the pulley is at the reference point mark and adjust the second cylinder in the firing order. Do this turning the engine 180 degrees each time till the next pulley mark is at the reference mark until all four cylinders have been adjusted or checked. This procedure keeps you from having to find the compression stroke on all the rest of the cylinders.
I personally have never installed it backwards but I have heard that it could be done. (Heard stories of people having to resplit the tractor. What a pain) I notice and take note of the existing configuration before I attempt a swap.
-Andy