vacume pipe (the small one on the back of the tap)
That's correct
Any way to check the vacume pipe is working correctly before I strip the front end?
If it was working fine before there should be no reason why it not working now, but you may want to check the other end of that hose has not been accidently pulled of the rear cylinder. You can see it on the v side of the rear cylinder from the left hand side of the bike. There will be a nipple coming out the cylinder just below the carb inlet rubber that it attaches to as follows:
{edit} Oops I just realised this is a pic of the front cylinder not the rear, but it's the same on the rear and I have a pic further down that shows it clearly.{/edit}
Rear cam sprockets in your pics look good. where the cam lobes pointing upwards and inwards like the following:
Taking the front cam cover is not as bad as it sounds. It's just a pain because the fairing and carbs need to be removed.
1) remove front fairing, I assume you know how to do this. Remove mirrors and a few Allen bolts on fairing.
2) remove airbox and carbs. instructions here
http://vtr1000.org/phpBB3/viewtopic.php ... bs#p217221
2) remove the plastic cowl that sits below the carbs. This is held in with plastic trim clips. Note how the TPS cable and the smaller plastic bit fits where the throttle cables run through.
3) From the front of the bike behind the front wheel, remove the two bolts that hold the Oil cooler in place. Then just pull the cooler down out the way.
3a) You may be able to gain access to the bolts on the cam cover now.
4) If not then remove the bolts that hold the rad in place and just pull them out the way like you did with the cooler.
5) you should defo be able to gain access to remove the front cam cover now.
Should take you around 20mins.
Once you have set the timing to FT on the flywheel the cam lobes should be the opposite to the rear and pointing upwards and outwards. Sorry I haven't a pic of that. Check the marking on the cam sprockets are horizontal with the casing FI and FE.
Here's a couple of pics with both the cam covers removed.
carbs and plastic cowl removed. You can also see the vacuum hose on the right. Note I have an extra vacuum hose that comes of the front cylinder for carb syncing purposes.
Hope that helps.
(:-})
that's not good mate. I'm surprised the bike turned over and started. That would put a lot of stress and strain on the rear cylinder. Surly the the tension would be too tight for the starter to turn. 
Did the bike struggle or turn over slowly when starting? I'm hoping I am wrong and I'm sorry to have to say this, but I think you need to do a compression check to make sure that no damage has been done here and rule it out as the cause of loss of power.