I managed very little yesterday, not enough to post, and so finished it off today.
So here is my solution to the drilling problem I had. Notice the word HAD, you will see later. You should see it develope as I go along.
First off, I needed a bit of tough material, because I only have 180+ holes to drill, it isn't worth hardening anything for such a small quantity. I found a lump of stainless off some sort of machinery I must have stripped down at some time. A spigot to fit into the bore was turned on it, and polished so that the bore wouldn't be damaged.

A very nice sliding fit, but not loose.

This is a pic of the drawing showing how the holes have to be, but because I am working with round bar and not square, I couldn't use the marked positions for the holes. Instead, I worked out the PCD of the two sets of holes. These dimensions will be of help to you if you use round bar.
The cover up of the drawing is because when I talked with Lance about doing this post, I promised him that I would not show enough of the drawing to allow the engine to be made. The plans and fixings are very reasonable, and it would be expected you purchase them if you wanted to make one.

I needed two plates making, one for either end of the cylinder. One end was drilled 5mm, the other drilled and tapped 5mm. Sorry about the metric, this post was supposed to be all imperial, but at times it will need to be. Most of my workshop fastener stock is metric. The discs need to be larger than 1 3/8", and mine are about 1/4" thick. There is a reason for these dimensions, but they are not overly critical.

This is what they look like with the cylinder loaded.

So now I had to get things onto the RT, to get the holes drilled in the right places.
First thing is to centralise the RT to the quill and get everything zeroed up.

I fitted the disc that goes onto the head end of the cylinder first. This uses the smaller of the above PCD's. So the Y axis was offset by half the PCD figure, and the standard 0,90,180,270 degree RT settings were used for the four hole locations.
These positions were then centred with a #1 imperial centre drill (1/8" diameter, this is a diameter that is used later). As this is a bit of tough material, I used tapping oil as the lubricant.

The centre holes were then followed down with a good quality 1/8" drill. We need good sized holes here. Make sure you stand the piece off the chuck jaws slightly, otherwise you will drill the jaws as you break thru.
It was at this point, I stopped yesterday. Unfortunately, I forgot to take shots of the next two procedures, but the picture below shows what I did.
I locked up the RT really tight, and traversed some more in the Y axis, then machined a flat on the back of the disc, just like below. Coming in by 1/8" should give you a fairly wide flat. Make a note of the amount you come in, to the nearest thou.
I did the second disc the same as the first, except it was at the larger PCD. But before cutting the flat, the disc was rotated by 45 degrees.

This is what the second disc looks like with the holes rotated by 45 degrees to the flat. The flat was machined to the same setting as the first. I actually went to great lengths with my offset for the flat, because my jig is going to be used for a critical second operation. More of that in the next post.
Both discs had the outside ends of the holes countersunk slightly with a #2 imperial centre drill. These should be a 60 degree countersink, the same as on a #1 centre drill.

This is now the drilling jig itself completed.

And this is how you set it up.
Make sure you have the correct end in the jig for the pcd on the discs. Assemble it lightly, gently tighten up the vice, and the two flats should automatically be lined up perfectly, tweak up the screw, and you have the assembly ready for drilling

Or as I do, push the two flats down onto a perfectly flat plate, and tighten up.

Now set up a #1 centre drill (1/8" diameter) so that only the tip drills into the part, it should stop just before the countersink starts to cut. Then set the width of the vice jaws just a little wider than the washer under the assembly bolt head.
It is then a matter of just placing each hole under the drill and bring it down. The 60 deg countersink will guide the finger held jig and the centre drill into perfect position. Just carry on and drill the hole. Once you have done one end, flip over and do the same on the other end.

Eight perfectly placed pilot holes, exactly 45 degrees rotation between the two sets. It took less than half an hour to pilot drill 23 cylinders, over 180 holes. To do the same thing on an RT would have taken hours, mainly because of setting up for the 45 deg offset. Even if you used the square bar and tried to do it in the vice using a backstop, it would still have taken a lot longer. BTW, you cannot drill both sets of holes from the same end, the area for the cylinder fins get in the way of a centre drill for drilling the larger PCD flange holes. I suppose you could make up a special very thin pilot drill, but then you would have the trouble of drill tip wander.
I could have used the PCD function on my DRO, but you would have learned absolutely nothing.

Now comes the dead easy bit. Make up a close fitting stub mandrel that just clamps into the vice, you get it perfectly upright by putting one of the cylinders over it and making sure the cylinder end is resting flat on the vice jaws, then tighten up on the vice.

Put the small #1 centre drill in the chuck, and move the table until the drill tip goes nicely into the pilot hole. I would suggest the flange end first, as that is a straight thru hole. You can position the drill in any position you like, as long as the tip enters the hole precisely. This allows you to put it were you can see it the best.

Swap out for the correct sized drill, turn the cylinder until the pilot hole is under the drill and just go for it. Basically everything lines up perfectly and you can actually take your steadying hand away, only needing to steady the part when the drill breaks thru.
You do the head end the same way, but you also have to put in the smaller drill size and set your depth stop for the drill.

Again, about half an hour for all these holes. They almost drill themselves.

This is a close up shot showing the top and bottom offset holes. The smaller ones will go onto the tapping stand to have the threading done, and the flange end will use the drilling jig to set it up for squaring off.

Nearly at the end of making the cylinders, just square off the end and then onto the lathe for finning and trimming to size.
Bogs