Timing Mark Alignment

I just got done installing some new shims for the valves and am having the worst time trying to get the timing marks to line up properly. When I install the camshafts lined with one another and the line through the peep hole in the engine side case, as soon as I go to install the tensioner, it seems to just throw everything I just lined up off. There are two marks on the side of the engine, and from my understanding, it needs to be the single line. There's an "H" mark though. Should I line up with that?

Thank you

I don't have a WR-250X Service Manual with me, but on every other Yamaha I've owned, you go by the single l mark.
The H mark is actually a range of a few degrees of crankshaft rotation where the timing marks should be when using a strobe light to check ignition timing with the engine running at a specified RPM.
Get a Service Manual for your bike.

I've read your engine has been through a few hands and has some milage on it.
Has your cam chain been replaced with a new one?

I'm sure you've become familiar with how the Yamaha model codes work, now:

WR-250F = model designation
X = 2008 model of a Yamaha motorcycle, ATV, or scooter
WR-250FX = WR-250F, 2008 model

and:

WR-250X = model designation
Y = 2009 model of a Yamaha motorcycle, ATV, or scooter
WR-250XY = WR-250X, 2009 model

All of the Japanese motorcycle maufacturers get in on this method of using their own factory-approved system of describing exactly what the model and year of the unit in question is with these little code letters and numbers.
It's precise, but the fact is, lots of dealership employees don't learn it.

Thanks for the feedback. I have the e-copy of the service manual I downloaded here, which included some additional steps for removing the camshaft sprockets and putting them back in on the chain install. That isn't necessary for a valve adjustment, is it? The thought crossed my mind that the chain may be stretched, but in taking up all the slack I can (tensioner removed), I can just barely get both camshafts installed and moved around until their marks line up, which is I assume around proper tension during this step (correct me if I'm wrong here).

To try a different strategy, I installed the tensioner to where the bolts are just barely in, so that it can just slide back and forth. While at the same time putting one hand on the camshafts to hold them in place, and holding the rotor in alignment with my socket wrench, I slid the tensioner back in and was able to take up additional slack without moving everything out of sync. I then bolted the tensioner in all the way (locked position) and rechecked to see that the lines were still in sync, check. However, when putting a great amount of pressure on the chain with my hand and turning the crank, the exhaust cam seemed to get caught in place as soon as the lobes made contact with the lifters, causing the chain to skip teeth on this cam. I'm assuming you don't have to be the Hulk to hold this chain in place, so I'm thinking the lifter may have just been stuck somehow. By that point it was 2am and I needed sleep.

I may end up just taking it to a different (qualified) shop to finish this step, however I'll check the lifters and try a few more times first. Hopefully this feedback may help someone else mindboggled by this step in the process.

Good idea to enlist a shop with a good rep to have a look if you're unsure.

Ok, so I figured it out. I didn't have enough slack taken out of the exhaust cam side, and the other issue was turning the crank with the spark plug still in. Once I got a handle on these rookie mistakes, everything was tight and in sync.

Glad to hear it.

Also glad you came back and posted the outcome and reasons - lots of guys will pose a question, get suggestions, and - POOF! - you never hear about what happened.
I like to learn about these situations, too.
That's why I reply. ;)