I've never flushed from the bottom, only the top. A tip to not cross threading that I learned here on the Cafe is this.

After flushing the forks, re-install the fork tubes in the triple tree about an inch or so high as a way of holding it (a vise clamp). Without the springs or spacers installed, place the fork cap on the tube and slowly rotate the cap Counter-Clockwise until you feel the cap drop as the threads line up. Mark this position with a sharpie.

Go ahead and add your oil, springs and spacers. Line up the marks you made so the Fork Cap is past the drop in point about 1/8th to 1/4 turn and push down with the appropriate socket (preferably a 6-point) and ratchet and rotate CCW until you feel it drop and the treads line up making sure the cap is even with the tube and then rotate Clockwise and the threads start and then tighten the caps.

There is a Link to the Service Manual in my signature. You can download (recommended) or view online. The whole process is in Section 13.

I used Dextron ATF to flush my forks as it is cheaper than fork oil and then add fork oil.

 

The problem with doing as MPD suggests is that the amount of force needed to push the cap down can topple the bike off of a jack and maybe even a stand. My suggested process is similar to what MPD lists but keeps the fork off of the bike. Specifically, I recommend the following be done but would welcome suggestions from others.

I recommend NOT using the bolt at the bottom to drain the oil. How then would you refill the fork with oil and know you have the right amount of oil in the fork? This bottom bolt is NOT a drain port. It holds some internal parts of the fork in place. Replacing the fork cap is difficult and the threads are very fine and are soft aluminum so they can be damaged. So what should you do? I recommend the following. Remove the fork cap to drain the oil and access the "guts" of the fork. Follow the instructions in the service manual for cleaning, filling, etc. When it comes time for the last step which is to replace the fork cap, do this as follows:

1) Get two people to help you.

2) With the fork spring spacer NOT in place and the forks fully extended, there is no pressure on the cap so you can easily put it in place on top of the fork tube. Place the cap on the fork tube and turn it the WRONG way. That is, turn it as if you were removing the cap (counter-clockwise when viewed from above the cap). Do this very carefully and gently.... like a safecracker turning the dial on the safe. At some point, you will feel a click and the cap will drop very slightly. This is the point at which the two sets of threads (cap and fork tube) have aligned. Turn about 1/8 inch further - still in the counter-clockwise direction - and stop. Then scribe a vertical line on the cap and fork tube with a magic marker to mark this position.

3) Place a box end wrench on the cap nut. Have one person (probably you) work this wrench.

4) Place a rough surfaced wood dowel on the top of the cap nut and have a second person ready to push down on this dowel. This should be the stongest person present.

5) A third person holds the fork tube upright and fully extended.

6) When ready, align the two marks made above in step 2. Lift the cap, insert the spring spacer, and replace the cap taking great care to get it back in the exact same clocking position as before the spacer was added. With the spacer in place, the cap will not be able to easily touch the fork tube so you cannot easily see if the scribed lines are aligned.

7) have the dowel person push down really hard on the cap. This should be able to bring the cap threads into contact with the fork tube threads. When in contact, keep pushing down hard with the dowel. The person with the wrench should then verify the black scribed lines are aligned and begin tightening the cap with the wrench. Take care to do this smoothly and feel for any grinding, grittiness, or difficulty turning the cap. These would all be signs that the threads are cross threaded. If cross threaded, back off the cap and start over.

8) Once you reach a point where you have turned the cap one or two full turns without feeling any cross-threading, you can remove the downward dowel pressure and finish tightening the cap.

9) There is a bit of skill/art needed to accomplish the above but it is totally doable by a reasonably skilled amateur - someone who knows what a cross-threaded situation feels like and can sense this.

 

A clamp and a saw horse, a long strap and with the strap around the top and bottom
then easy to turn the tube while the cap will click in. I was fighting it until I remembered this tool.
The PVC pipe allows turning better.

I rinse with diesel oil, then cheep Dexron ATF, then Synthetic Dexron.

The first fork oil change was low on oil, fuzzy stuff, stunk real bad.
Honda did not specific a fork oil replacement time.
The next fork oil change did not stink, oil change level was good.
190,293 miles 4/23/2019 Fork oil change after 7.5 years and 76,100 miles.
NO STINK from the Synthetic ATF I put in Sept 2011. No grease like build-up on the springs.
About 13 oz returned per fork.
New clean and refill, Dexron ATF Synthetic which is 10wt or so.

 

Thanks for all your valuable inputs - only a few weeks left for riding out here in Ontario - will enjoy the fall colours and will leave the forks as a winter project - will provide feed back once all is done.