For the relatively simple LS650, all you do is line up the mark on the end of the cam to the top of the cylinder head at TDC - it is not rocket science.

With the Wiseco and DR650 cam, you should have noticeably more power than the stock piston and cam.

Do you have the ability/equipment to do a compression test?

The OEM DR650 cam runs just fine when set at the factory marks.  There's no need to try and advance or retard the cam.

Check your carburetor and make sure the slide is lifting all the way when the throttle is wide open.

Verify that your oil level is correct.  Make sure it's not over-filled.

The compression check is a good recommendation.  Make sure the throttle is wide open when you check the compression.  If your cranking pressure is below 190 psi verify that your valve adjustment is not too tight.

Did you make any other changes when the cam was installed?  A different air filter, exhaust system, etc.?

There are tons of ever so cool looking air filters that also manage to block air into certain parts of the carb, creating all kinds of issues.

With the mods that you've done it should run noticeably better than stock.  Lots better.  You said it ran better before the mods.  Was that with the reverse cone muffler?

Your main jet is in the ballpark.  You proved the air filter isn't chocking off your WOT performance when you did the quick & dirty check (ran without filter).

If your compression checks out good then you probably should check cam timing.  That requires removal of the head cover.

Years back, I did a top end rebuild on a 305 Honda. After I was done it ran like crap and very rich. It turned out I had the valve timing one tooth off.

Remember when doing the compression test that you must disable/disconnect the compression release cable and hold the throttle wide open.

I assume this will be a leak-down compression test and not just a psi test. One is diagnostic and the other is nice information, but doesn’t lead to conclusions.

So now you have confirmed that the compression is where it should be.  With that DR650 cam and Wiseco pop-top, 200 psi is right on.  

You ran it without an air filter so you proved that the foam filter you are using isn't restricting air flow.  I assume that the performance did not improve with the filter removed.

Did you verify that the carburetor slide is opening all the way (as previously suggested)?  The VM38 you are running requires a lot of twist grip to fully open.  Look in that carb and make sure the slide opens all the way.

The 210 main jet is pretty close to where you need to be with that combination of parts.  What can you tell us about your "18" reverse cone with baffles"?  Where did you get it?  Who manufactures it?  What sort of baffles?  Post some pictures.  Take the baffles out and take pictures so we can see what you've got.  Might be a case of constipation.  Your bike should run well north of 95 mph with those engine mods.

You mentioned that your bike "struggled to hit 6000 rpm in 3rd" and your comments about fuel consumption imply that its rich .  You can try leaning it out with a smaller main jet but you must be careful not to run it lean in the upper gears (3rd & 4th).  Tell us more about your VM38.  Where did you get it?  What needle jet is in there?  What slide needle?  You should have a 166-Q2 needle jet and a 6DP1 slide needle.

Is there any chance that your alternator rotor was replaced with one from a newer LS650?  Verslagen had some trouble with that.  I believe he had installed an older rotor on a newer bike which resulted in grossly advanced timing and high speed misfire.  If I got that right, then a newer rotor on your older bike would result in grossly retarded ignition timing.

As previously mentioned, if all the above checks out you will need verify your cam timing.