David,
Installing TRS2006 along with SP1 does not take very long.
1) Install the program. DO NOT RUN TRAINZ AT ALL.
2) Install the SP.
3) Reimport all your content from your local folder.
I highly recommend moving the local folder before reinstalling as this will decrease the amount of time it takes for the program to patch. When the patches are installed, they go through all the content you have as it rebuilds the database. By importing your content after the patch, you are ensuring that the patching process completes quickly.
To bring your content in, use File Import Content. Yes there are other ways, like moving the folder and deleting the Assets.tdx, but I find the File and import content method ensures that the content is installed properly.
Depending upon how much downloaded stuff you have, will determine how long the process takes.
Regarding TS2010 and patching. It appears that you munged stuff up by canceling the patching process. Patching takes a long time, and it's best to leave the system alone. Afterwards run an extended database repair even though the program does so when requested.
Any errors that will appear in Content Manager afterwards, are usually false, and are due to the database tables not being updated. Select the content, and choose view errors and warnings. This will usually remove any extraneous/false errors you may have.
Email me if you have any questions. I can call you if you want over-the-phone help.
John