The pop bumpers lights are NOT flashers, so you don't have to worry about that much at least. They are 555s. I did a complete LED conversion on my R&B and put rainbow faders in the pops.

Also the OP may be referring to Z connectors like this:

http://bayareaamusements.com/Merchant2/merchant.mvc?Screen=PROD&Product_Code=CN-5791-12235-10

I bought a 6-pin one and just snapped off the extra pins I didn't need.

With regard to the kicker, you might want to make sure something else isn't crossing into the line feed (including the ground braiding). I had a strange issue one time when both flippers started acting crazy. I traced the problem to an LED that had been poorly manufactured to where a line of solder was touching the center and shorting it. People SWORE to me that it wasn't possible for a bad LED to affect the flippers like that, but as soon as I fixed the LED, the flippers worked fine after that instantly.

Here's the one I bought:

http://www.pinballlife.com/index.php?p=product&id=2887

They have 4 and 2 pin versions as well.

VUK rebuilds are easy. I did the Super VUK on my R&B, and the only issue that came up was the kit I got had the wrong size hole in the plunger rod. I had to get a drill bit the same size as the locking pin and enlarge the hole using that.

Also just to point out, the Aesop hole Super VUK is notorius for taking more than one try to eject the ball. So that's not really an issue with your machine. I will say that after I rebuilt mine, it does seem to work more consistently.

I've done a full strip down of the playfield when I restored mine (without a rotisserie). The trick to the ramps is the ball diverting arm has to be removed from the linkage underneath and then slid out the top (of course being mindful of the collar that will catch on the plastics if you just try to pull it through). Once you get that arm out, the rest is a simple strip job.