Haynes really isn't the right resource for these vehicles. Bentley is what you want.
There are THREE things that have to be "lined" up: Crank, IP AND Cam. With the proper tools (you haven't said what you used) you're "indexing" things (folks say they are "locking" tools, which they really are not). IF you get everything indexed, and assuming there's no other issues with the engine, then the engine will start without any problems (I have about 40k miles on my car, my first TB job, and I have never touched the timing since that job- it shows up, using VCDS, exactly where I would want it to).
You did not say that you replaced the O-rings on the Thermo Tee. I mentioned this but you did not respond to identify whether this is still an issue to be concerned with or not. NOTE: you REALLY have to specify things in good detail- we're all out here in Virtual World, we cannot assume anything, we have no way to see or touch your car! you're being a "Newbie" makes things even more paramount that you communicate clearly (no cutting corners).