Rotating the cams.
 

I have looked through a bunch of treads but cant find any info. I think I am going to line it up and loosen my cams and spin them into proper position and tighten.

Found info but I dont see what you see.... I have a mark that says rt and the other says just F and a blank one. I know the blank one now is tdc. The rear cam is fine. The front when I set it using the f all 4 valves hit the piston. I am in a world of hurt as I am sure after removing the exehaust that the valves are not bent. I am going to try to line them up to the blank space now.... FML. I wish I had done the stopper mod when I did the carbs...
EDIT:
Foooooked... Valves were bent open thats why the timing wont line up! Post pictures as soon as I get my phone... I think a trip to the dealer is in order. If he throws me some free valves and a cct I wont kill.

Did the dealer mess it up? Why were the cams out of position in the first place? You kind of suggesting it was the CCT but I can't tell for sure.

cct failure after they said it was ok. they said parts or labor but he got me the valves cheap so I am going to do them my self and make diy ccts out of the old ones.

The stock CCT won't show any signs that it is bad, until the spring snaps. Your dealer would have no idea.

On the VTR1000.org site, someone had a stock CCT let go at 6,000km (I think that was the lowest) or it could happen at 60,000km. You can't predict it.

Another option, is to buy a good used head off eBay or the likes and simply swap heads. Much faster, since you mentioned needing this bike for transportation to your work.

As this is not the first time this type of incident has happened, it should serve as a warning.
There are good mechanics and there are less than good mechanics. Even the good ones can make mistakes when dealing with a machine that they are unfamiliar with. The not so good ones can really make some disastrous ones.
While not everyone has the desire, ability or the space/tools to work on their bike, a large amount of caution should be applied to turning your bike over to someone else to have work done.
A cross check of what a mechanic is telling you and what is known fact here on this forum should be done.

I dunno front seemed all loosey goosey sounding to me. Valves are on the way. I just gotta have someone with a machine to pop the old ones out. Stuck in so bad the keepers wont come out with the good ol fashioned socket method.

Im going to keep working on my cf tail until the valves are back then a quick port and some diy manual cct action.

This post can be deleted if a mod prefers it.

But as an update. youll never time your bike with broken valves. She indeed runs strong. Following cybercarls guide on vtr1000.org

You dont need a set of cant think of the name but various thickness pieces of metal to check if the valves are gone. The cups wont be anywhere near the cam if they are super bad. If you cant see it stick something thick in there like a screwdriver head. between the cup and the cam. if it fits they are Fooooookkked.

You can not hammer out valves that are super bent. The spring pressure is too high. I actually bent the tool getting one of the valves out.
Lapping valves should be checked by someone who knows how to do it. let them show you. dont read some guide. Advice to check if it shuts is a dab of oil based paint around the valve stick it in and spin it. the paint should be forced out and leave a super thin film in the metal grain. Then use fine paste to make it nice and smooth.
Put the keepers in and whatever shims get you close. They WILL NOT meet spec. You will have to touch some material away from the top of the stem. Valves are hard material and take quite a few seconds to remove the material away. IF your not sure or dont have a mini belt type grinder DO NOT DO IT! have a buddy do it. MEASURE MEASURE MEASURE! If your a hair tight its fine aka 1 thou. If you have a gap of 2 thou you are also in spec. but I would carefully get as close to spec as possable.
BTW: I ran honda 2.00 shims intake and 1.952 exhaust. Stock honda shims. One last note if you have a caliper thats not amazing zero it every time. my right valve is shorter than the left by .005 its not enough to cry about but its not cool. My mic auto zeros. Most dont.
Bike runs great.

You do know that, you can get valve shims from companies like Hot Cams, right?

After doing complete head work and then installing new cams, I knew that I would need new valve shims. So, I ordered from this company HONDA VTR1000F SUPER HAWK 996 HOTCAMS VALVE SHIM KIT | eBay

Made it very simple to get my valves within spec.

A lot easier, yes?

Always used hydraulic cups. ( Forgot what they are called.) I also always had a machine shop do the valve installation for me. Honda didn't have a good shim ready made. I would have used the above link but I was short on time and money. I noticed my vlaves had been ground a bit to match anywho whole thing took under an hour minus the lapping in.