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At half throttle and when decellerating, all I get is pop pop pop pop pop. To put it in context, i just bought her and rode her home (2 miles) shop owner said she sat for 2 months before selling. She didn't want to run at the shop, had to stay on choke for 5 minutes on a 92 degree day. Put a half tank of fresh gas to offset the old gas, ran a little better.
Yesterday while putting the new tags on the bike I noticed that the po drilled holes on the stock mufflers inbetween the outer casing and the inner outlet (when looking straight at the end) My question is: is this leaning out the bike too much, or is this simply an old gas problem. (drain, refill, replace plugs). Honda has an emission control valve that draws air into the header, and I read that this makes a slight popping sound that some mistake for backfiring. That valve also makes it hell to rejet after modding the exhaust, so I would rather bring it back to stock.
What should I look at next?

Sorry,
2006 Honda vt750 Shadow Spirit w/ 12k miles

Well, first guess would be that it needs re-jetting (or re-mapping for EFI), or get some stock exhaust back on it. Second guess is fouled carbs from sitting.

Unless you got a helluva deal, it should never have been sold running so poorly and with old gas in it.

There are the obvious things you should check thoroughly with any previously owned bike, of course: plugs, electrical (especially ignition) connections, etc.

First step will be finding the Clymer's or other shop manual for it.

Keep us posted....

2006 was still carbs, now they are FI. Took it for a short ride yesterday with the half new gas (haven't drained and refilled it yet) and it warmed up faster and backfired much less, so I think drain, refill, and new plugs will do the deal. I am sure that economy is probably affected and a little backfire will stay if I don't plug the holes.
Is there a way to plug the 3 holes in each muffler to bring it back to stock (they are Honda muffs). I was thinking maybe tap the holes and use machine screws so I could remove some later if I wanted to. At first I was thinking jbweld, but I don't know if it gets too hot.

If they're (the holes) small enough you could use pop rivets.

You also might check the local dealers for any extra sets they may have after somebody put aftermarkets on their bike. Also check craigslist, e-bay, etc. for the same.