The ORINGSTORE sells 4mm O-rings that may fit inside the big nut. They also sell a 4.5 mm CS and a 5MM CS. Check the sizes below in the first three thumbnails. I am assuming the inside diameter of the o-ring as 30mm based on your measurements.
As for the release stem seal, Lazzar's (HCRCNOW.COM) sells one seal that is intended for the mini jacks and others, but it might work in yours depending on the measurements. They give the measurements in the page the item is shown. Check the link below. There is also a pic of it way below.
http://www.hcrcnow.com/shop/parts/hein-werner/featured/8846
Otherwise you will need to find some rubber vacuum tubing of the same size, or any other rubber hose, to replace the seal. Still, the stacked O-rings idea should work, as long as these keep the necessary squeeze between the stem hole and the stem itself. It should work like any other o-ring application. O-rings come in 1.5mm, 1.6mm, 1/16", 1.78mm, 1.8mm, 1.9mm, 2mm, 2.4mm, 2.5mm, 3/32". If you check TheOringstore metric o-ring section, you will see more small cross section sizes, although a couple of them do not have smaller ID sizes to fit over the stem end. The ones mentioned above have smaller ID sizes to fit over the stem end. Anyway, you need to measure the CS of the rubber tubing you removed, maybe add some small percentage to that measure to account for wear, and see if any of the O-rings above matches the CS of the rubber seal. Link to O-rings.
http://www.theoringstore.com/index.php?main_page=index&cPath=368_12
Could you measure the pump piston u-cup Outside diameter? Also, the top part of the pump piston diameter, as shown in the pic below? I was thinking that by subtracting two millimeters (one per side) to the top part measurement, the inside diameter could be obtained,
maybe, as I don't know how tall is the edge that retains the u-cup in place. I will assume it is at least 1mm. And also, please measure the height.
About the dust boot, if the pump piston could be taken apart it would be easier to fit some type of bellows, maybe like the ones used in rack and pinion power steering where the shaft that pushes the steering knuckle comes out. Some of these bellows might be small in diameter to fit over the pump piston cylinder. Or maybe one of the small boots used in ball joints or rod ends. But this would remain static, unlike a below, so the smaller hole fit should be loose enough to allow the pump piston to slide in and out easily.
Let me remind you that the proper names to use here are u-cup and o-ring. You don't have a "rod seal" here, except maybe for the release stem seal. If you contact someone and ask for a "rod seal" you may have a though time getting what you really want. I get somewhat confused, even though I know what you are talking about!