I'm sure there are tons of information on this problem... I've been reading a lot of the threads, but still not decided what to do next.

My 2006 RS 1700, was in the shop in Dec to put V& H Powershots on it. With the OEM pipes, I always had to choke it for at least 5 minutes and ran it that way before it warmed up and could be turned off.

The Yamaha certified mechanic said with the new pipes (Has a K&N air filter box/set up already of it.) that it was running lean and so they put a jet-kit in it. It ran good for a couple of weeks and the power was great. Then it began to have starting problems.

For one thing, now I cannot use the choke at all. I can get it started but it will not idle long enough to warm up, so I'm left starting it, die...starting, die (throttle will not fire it up or rev the engine like it should, it just dies.). This happens until I completely drain the battery, trying to get it to warm up and idle.

I had it towed to another dealer after trying new plugs. They said they could find nothing wrong with it and it started for them. ???
I picked the bike up and it was warm, so it ran OK. When it really warms up, it will idle a little high. (So I adjusted the idle screw [barely], so that it was better at idle. The next day, we were back to square one. It would start but would die after a second or two. Start, die, try to keep running by revving the engine but no go. Now the battery is dead and need to have someone (who knows) fix this problem, but don't know what to tell them to help them out. (Float adjustment?, fuel pump? Stator? What?) And why won't the choke help out now, with the new jet?

Battery is on the charger again!

Just so I understand. You had an open filter Barons BAK with stock pipes before with stock jetting? Now you have The BAK, pipes, and the dealer jetted? First thing you need to do is find out what jetting you have. Main jet, needle, if they changed the pilot jet, what the PMS is set at.

If they are like most dealers you are jetted too rich. That could account for why you don't need the choke. Are you twisting the throttle before you try starting it? If you're trying to rev it up while it's still cold that probably won't work. These bikes aren't happy until they're warmed up.

Sorry, it has a K&N filter/box set up on it, not a Barons. (The OEM pipes and it were fine.) I think it is too rich too and told both the original mechanic would put the pipes on it and the second mechanic said they thought the float bowl needed draining, etc., but then said it started right up for them. I know this bike is really cold natured. The first mechanic said, I would have to re-learn how the bike ran... what the heck?
Do I turn the gas on, Twist the trottle, start it and then what happens when it dies...

But it is an open filter airkit? Not just a filter and cover that replaces the stock and completely encloses the filter? That's important to know. You need to go in the carb yourself and find out, or get the mechanic to tell you what they put in. We need to know that before we can tell you what to try next.

Ok, thanks.
The bike has just the filter and cover that replaces the stock... and encloses the filter. (It says V 102 cub inc on it.) You can see it on my profile.

In that case they shouldn't have touched the jetting and that's most likely what's causing your problems now. Shops love to do this to people. You need to go back to the stock jets and needle or get an open filter air kit and jet the bike again.

if you don't need choke, then it's too rich. don't need to jet for pipes only, pilot screw adjustment and remove the AIS. You also shouldn't be using full choke for that long, you'll foul the plugs, full choke to start about 30sec, then about half for a min or 2, will depend on how cold temps are. and it's better to feather the throttle then to keep choke on for 5min. Like Musky said, you should go back to stock needle, stock main jet and stock pilot jet if they changed that as well.