I just rebuilt the carbs in my bike about 4 or 5 days ago.  I got the bike and it was rejetted with a K&N lunch box filter.  I replaced the plugs and I believe I have the bike running alright.  It has 16,6XX miles on it so I don't expect it to run perfect.  Well I have put about 160 miles on it since the rebuild and today was my first day on the highway.  For the first 10 or so minutes in 6th gear pulling 70mph ~6000RPM the motor started to bog a bit, feels like it was breaking up on me.  It would start to lose RPM and then surge back to where the throttle was held, and then do it again.  This happened for about 3 miles before I got off my exit.  I am not sure what that could be, really.  Since I have done everything for fuel and air to mix right, my next look would be the ignition, but I don't really know how to check it to see if it is working correctly.  Is there like an OHM reading I can take to see if the coils are holding enough power?  

I checked my float height and it seems right now 14.6mm or so.  It has no shims on the slider needle, but I am not positive I need them.  Do you think it could be starving for fuel at a steady RPM like that?  I am lost a bit here.  I get a hovering idle every now and again, but not much.  I expect this thing to not be perfect, but I would like to make the commute in it without me worrying about it making it(~20miles round trip).  

try switching to prime. these bikes are notorious for fuel starvation at highway speeds. if switching to prime helps the problem, than you know it's the fuel starvation issue.

there are a few mods people have done. look into it if you want =]

Really?!  I have seen the petcock mod threads on here a lot. 

Thanks for the advice.  I wouldn't think it would be like that only at highway speeds.  I'll go give it a try now. 

yeah the vacuum actuated diaphragm can't open wide enough for proper fuel flow at high speeds (high speed = more fuel needed) or at least, that's the way i see it. im sure there's more technical ways to describe it. or even a way that's actually correct and not just my assumption. =P

but yeah, on the highway i tend to always ride on prime. i also try to fill up every 100 miles if possible. annoying, but it's better than being stranded.

Well I didn't even get to the Highway before it broke down on me.  I set the petcock to "PRI" and half way to the highway it started to choke itself out.  So I moved the Petcock to "Fuel" and it started to run normal again, then I tired the "RES" position and it died completely on me.  I had to try and physically prime the motor by moving the main fuel like up and down to get whatever fuel was in it to the bowls.  Then I got it to fire while holding the started until it pulled enough vacuum to operate correctly then I drove it home...Sounds like a bad petcock to me, what do you all think?

Sounds like you're low on fuel and you have your lines crossed running from the fuel tank to the frame petcock.

Lines are crossed?  Would that still matter even if they were?  I mean, if I put the frame petcock to "res" would that really matter because I mean, they fuel is still getting to the petcock.

stock tank and petcock: the res function bleeds from a line lower in the tank than the on position. so if you need to be running on res, if you switch to on your bike wont have gas. but, because ON gives you gas and reserve doesnt, it's probably that your lines are crossed. the ON is running from the lower nipple, and now your RES and PRI are higher up in the tank.

that's what it sounds like to me at least.

get more gas and check your lines.

Great.  I'll go check out the lines.  I did put a shim (aka: washer) on the slider needle and that really helped things through the rev range.  I am not sure who rejetted this thing before I got it, but I don't think they took much time on it.  They also drilled the exhaust. 

I was reading a few other threads here and people were talking about the upper fuel "nipple" creating a Venturi effect if it doesn't have a hose connected to it, and it could cause a pressure difference on the carbs.  Anyone heard of that?