[platii]

But whenever I rotate the crank to tdc the intake cam is not facing straight up

Because you missed up the timing by removing the hex bolts WITH washers. You probably also missed up the timing of the exhaust cam gear by NOT installing a M8X18 bolts at the back of the exhaust gears.
The 3 hex bolts WITH washers on each cam gear are what hold the spring tension inside the gears. When you removed the hex bolts with washers before the timing tool installation the spring tension released and missed up the timing.
Now your duty is to return to point zero then to follow procedure again.
First you need to remove the Vanos adjusters (you remove the hex bolts without washers).
Next is to position the camshafts back to timing position with a wrench and tighten the hex bolts with washers to 10nm. During the process the sleeve of the camshaft gear must moved forward. The intake sleeve may be easier to move by hand but the exhaust(if you lost the initial timing by not installing the M8X18 bolt) might be hard. One creative member managed to pull the sleeve of the camshaft for the exhaust be installing long bolt from forward to back through the sleeve to pull the sleeve forward then he tightened the hex bolts.

If you managed to get there then you install the timing tool on the camshafts and continue the removal procedure properly.

I suggest you read the procedure again for the adjuster removal, cam gear removal, timing check, and timing adjustment to understand the sequence and how the timing process work. pay attention the notes, important notices and warning of injury.

 

[platii]

From last picture tighten the 3 hex screws on each cam gear to 10nm with the timing block installed as shown remove then remove the cam center bolt and lift the whole assembly(cam gears and timing block) altogether, then after the rebuild you put it back the same way.
Now since you removed the cam gears you need to put back the timing block between the gear sleeves to counteract the spring and extend the gear and tighten the hex screws with washers so the assembly is ready for installation.
You may not have difficulty to extend the intake cam gear but he exhaust gear is hard. There is a tool in TIS that you install it on the exhaust cam gear teeth to help align the teeth and counter act the spring to allow you to install the M8X18 bolt on the back of the exhaust gears, this bolt will stop the cam gear from retracting and allow you to put the timing block and tighten the hex screws to be ready for installation.

A member in the forum (other than me) after he installed the exhaust cam gear he installed a long bolt on the sleeve from Forward to Back in one of the sleeve holes to push the sleeve back and extend it then you can tighten the 2 remaining hex screws to hold the cam gear extended then he removed the bolt and installed the third screws. I think that what he did if I still remember, hope you get the idea and understand the timing position of the cam gears.

This is the tool picture:

What I think is possible to realign the exhaust gear

If you used long bolt to extend the exhaust cam gear to may not need to install the M8X18 bolt, just tighten the sleeve with the remaining 2 hex bolt with washers to hold it extended.

 

[platii]

Thank you @P-Chi for posting this.
@Sollsam , this is the position you should reach just before you release the central camshafts bolts then you lift the assembly as in the 2nd picture, set it aside until reinstallation.
The timing position is held by the timing block and the 3 screws with washers, both gear are extended, sleeves all the way to the right, screws with washers tightened all the way to the lift. "Yellow" bolt is necessary to hold the exhaust cam gear tensioned.
This step is the most important and difficult to understand, the rest is simple, just to set the camshaft in timing position using the camshaft timing tool.