OK first thing take your time (no pun intended) and don't rush things. This is how mistakes happen.
So let me get this right, you where on the rear cylinder and rotated the crank onto the front but have messed the timing as it has jumped from removing the tensioner on the wrong stroke as well as turning with the tensioner removed. But there is still an issue with the rear.
You need to deal with one cylinder at a time it's no good going back to the rear if the front is not correct and has jumped. By the sounds of it rotating the crank any direction may meet resistance ie valves hitting the piston. Have you tried rotating the crank around more
Slowley onto FT with both cam lobes pointing up and out? If you meet resistance you will have to loosen both cam caps so the valves remain closed. Undo these in a diagonal pattern a bit at a time.
Actually as both cylinders are possibly not correct it may be worth you loosening the cam caps for both cams on each cylinder and starting from scratch/the beginning. You have no worries about any valves meeting cylinders then. You just need to be careful to hold the cam chains taught and feed them around at the same time. A helping hand could be useful here as it's tricky to turn the crank and hold the chains at the same time. Or leave them wrapped around the cams which should spin easily with the caps loosened.
Start with the rear cylinder following the procedure in the guide. RT at the crank and then place the cams so the lobes point up and in with the RI and RE marks aligned at the cam sprockets. Start with the cam on the opposite side of the tensioner so Inlet cam, pull the chain taught and hook it over the sprocket. Then move onto the exhaust cam on the tensioner side. It may take a few attempts getting both cams aligned correctly with the chain hooked over them both. Once both cam are aligned correctly with the chain over them both tighten the cam caps back down to the required torque in a diagonal pattern a bit at a time. You may want to leave the two bolts off for now which the chain guide fits under. Go steady and don't overtighten them as they can snap
![EEK! :eek2](./images/smilies/eek.gif)
Then tighten the tensioner up.
Once the rear cylinder is done you can them move onto the front. Pay particular attention to the amount of turns on the crank. You want to turn the crank 1 1/4 turns anti-clockise until you land on the FT mark for the second time it comes around to the inspection hole. If you loose count or sight of where your at then just go back to the Rear RT with cam lobes pointing up and in and start again, it's crucial you get this right. Then run through the same procedure on the front cylinder accept for having the cam lobes pointing up and out and markings being FI and FE. Start with the exhaust cam this time as it's furthest away from the tensioner. The front is a little more tricky to align the cam marks as the frame gets in the way for the inlet cam. Once you have them aligned, yet again tighten the cam caps down to the required torque in a diagonal pattern a bit at a time and then tighten the tensioner.
If something does not make sense then ask first before moving on.
(:-})