I suspect the extra hole and shorter springs also work in conjunction with a K&N filter but that is only a guess. Loads of folk have had issues and much dyno time getting a K&N filter working with these bikes for some reason. Personally I would put a standard filter in as has been suggested previously. It's going to make things a whole lot easier and smoother to tune.Onto the mains.
Be careful with these conversion charts as it's debatable to as accurate they are. You don't think Dynbojet are going to give their secrets away that easily. Their jets are measured by flow rate unlike the others, so not exactly a fair comparison. This is one of the reasons I went the Factory Pro route because they use the exact same mains design and measurement scale as KeihinAnd checking the cross reference guide here;
viewtopic.php?f=9&t=35272
You cant compare Dynojets to others and unfortunately it's not as easy as looking at a chart and putting an equivalent size jet in place. There are no short cuts. You put what you think is right in (often the recommended baseline) and go for a ride at the appropriate revs/throttle position for the carb circuit your working on, in this case the mains. You then go up one or two sizes larger (richer) on the mains to see if the bike performs better and then go down smaller (leaner) one or two sizes and go from there. You may find that the original baseline jets work the best in which case you stay as is or try one leaner or richer if you went the two steps before.To answer your questions.
Stick with two 180 dynojets or possibly a 180/185 combination if running the dynojet needles. If you go standard you would be better off going back to standard needles or using a kit that use the same mains design. Stick with one or the other. You start mixing kits and it's going to make things tricky and time consuming to get right.1. I am unsure which main jets to get if getting genuine.
I don't recall the exact instructional guide that come with the kits but IIRC it says to use the shims. I would have a shim either side of the clip personally as it keeps the clip and needle more stable/securely in place in the holder. You could always go richer or leaner by moving the clip position anyway. So if using the the dynojet needles 3rd or 4th clip would be about right as long as the slides are standard and don't have the extra lift hole or shorter springs.2. Using the DJ needle with the clip in the 4th hole from the top, do I need to shim it as with the standard? Or just leave it as is?
If you want to stick with the K&N filter then you may have more luck with their springs and extra lift hole but be prepared for dyno time to get things right.
If you decide to go the standard route then yes jet r us are good. There should be firms closer to home for you that do jets though.3. Is jetsrus.com a good place to source the parts?
Getting back to the slides. Do a good job with epoxy and block the rear of the hole inside the slide so epoxy does not squidge through and make a mess. This will affect the needle holder and could add to weight distribution as the slide opens and closes. Get your filling as flush (smooth) as possible on both sides of the hole and make sure the epoxy is fuel resistant. Also don't mix the front and rear carb slides up if you can help it. They have worn into individual carbs. Were talking fine tolerances in carbs and you don't want a slide sticking or loosely chattering away.
If I was you I would go as follows:
Standard filter and stacks.
180/180 Dynojet mains
Dynojet needle (as you have it) on the 4th clip position and two lift holes in the slides as standard and run the standard diaphram springs.
(I bought new standard springs and they do make a difference. It surprising how much they shrink over the years)
48 pilots with 2 turns on the fuel mixture screws.
The above set up should get you dam close to spot on minus some light tweaking/tuning. I speak from my own and others experiences.
Something else that is worth considering while you in there is to get some new float needle valves. Only buy genuine as they are cheap to replace and a consumable service item kind of. The pointy rubber bit on the end where it sits in the seat wears down over time and leaves an indentation so sits lower in the seat which affects the float height and can cause fuel leaking past the seat. It's worth taking a look to see how worn they are if you fancy digging deeper into the carbs. Don't change unnecessarily though. Oh sh1t have I just complicated things
There is a lot more to carbs than simply dropping a jet kit in and following their instructions. 
(:-})
for a new Yuasa battery. That sucker better outlast me!!
