As you suggest, I will clean the engine and run it to check it over. The nut I used has the smooth flange as part of the nut. I will get some Suzuki bond sealant. Let the adventure begin!
Note: Incase anyone is interested:
M6 X 0.5 HS Plug Tap =  $4.60 each
M6 X 0.5 HS Round Die =$8.50
M6 X 0.75 HS Plug Tap = $3.60
From:
Victor Machinery, Inc.
33-53 62nd Street
Woodside, New York  11377
Phone: (800) 723-5359
Fax: (718) 899-0556
Email: sales@victornet.com

Bummers, plural,

It does sound like you need to take things apart and do an inspection to see what is healthy and what is sick.

If the valves are not healthy - they need to be replaced as they are very thin and have a surface hardening - they cannot be ground.  There are some India made aftermarket versions that are a bit cheaper than the factory ones.....not sure if they are good enough to use?  The valve seats can be ground if needed.

While the head is apart, it is a good time to clean up the ports and smooth out the restrictive donut in the exhaust port.  If you are unsure of the age......new valve seals are most likely worthwhile.

If the bore is in good shape, then a 94mm Wiseco can be used and will save you the expense and potential risk of getting the cylinder bored for an oversize 95/96/97mm piston.  The larger pistons offer a very small increase in power....the higher compression that all Wiseco pistons provide is where most the extra power comes from.  The stock 94mm piston makes 652cc, the 95mm makes 666cc, the 96mm makes 680cc, the 97mm makes 694cc.  So if we assume the extra compression takes the HP up from the stock 30 to 35 HP with the 94mm Wiseco, the 95mm would make 35.7, the 96mm would make 36.5, and the 97mm would make 37.2....so as an approximation there is only about a 2.2 HP difference between the largest and smallest Wiseco.  You should compare the cost of the different size pistons and the cost for the overbore is worth the HP difference to you.  (If your cylinder is damaged than an overbore will be necessary).

Camshaft - The performance camshaft is definitely worthwhile and it does make mor power.  The engine still is very mild mannered and has strong torque and you don't have to rev the engine to make things happen - as the camshaft grind is not very exotic and the engine still is smooth and docile.

Cylinder threads - While you have it apart look carefully at the 3 threaded holes for the long 6mm cylinder head cover.  These threads can be damaged and require the engine to be taken apart to fix stripped threads.  If there is any doubt - have Heli-coil inserts installed while the engine is apart.

Verslagen head plug - Buy and install the Verslagen head plug cap instead of the stock rubber/plastic one.

Cam chain - If the cam chain tensioner is extended close to the 20mm maximum, buy and install the nitrided cam chain from Lancer.

Assembly RTV - Buy and use the Suzukibond or Threebond, don't buy generic gasket maker at the big box or auto store.  The original stuff works better and is easier to use.  

I also believe the poor cylinder head design is a big reason that the LS650 is 30HP and the DR650 is 50 HP.  Going to a bigger piston will likely get you an equal increase in low rpm torque - but with the poor flow in the cylinder head you will likely not get an equal increase in upper RPM horsepower.

The bigger piston may just get you to the place where the head flow suffers and bit sooner than a smaller piston does - a smaller piston engine may run better at higher rpm than a similar big piston engine.

If you spend most of your time at lower rpm....maybe the bigger piston is better.  If you spend a lot of time on the interstate........maybe a smaller piston engine is better?

I thought Vesrah was made in India?

Anybody know how they stack up against the Suzuki stock part?

Status update on 2003 LS650. Did get bike running, didn't sound good. Adjusted the valves, better...but not good enough. Long story short has low compression, 85 psi holding throttle wide open. Now going the hard way and have parts all over the garage. Waiting for piston, tensioner, etc.  Hopefully, I can get it back together correctly. Fortunately for me, I have a secret source for information putting LS650 bike together...

Good point, yes I did. If it would have been 120 psi I think I would have tried using bike for awhile to see how performance would be, but at 85 psi not anywhere near good enough.