Spotlight data size to big
It seems perfectly normal. If you have deleted files from another OS, if you want to get back to stability, boot to recovery HD and repair the OS X partition. Then boot to OS X and download the latest combo updater and reboot.

I'd add the Mac partition to spotlight's privacy tab and close system prefs. Then I'd remove it from the privacy tab and let it sit for about 30 minutes and then run the combo updater.

As long as you have a backup of your files, worst case is you'll end up with a corrupt OS X side and have to wipe and reinstall. If you want to download the latest OS X installer during the 30 minute wait above, it's nice to have it on a USB thumb drive just in case. Probably you won't need it as the spotlight system cleans and takes care of itself fairly well. The only times I've seen it have huge files is when the system gets modified externally as you describe.

Here is some data to back up my opinion that 900M isn't abnormal:

MacPro:~ bmike$ sudo du -sm /Volumes/*/.Spotlight*
2952    /Volumes/Backups/.Spotlight-V100
496     /Volumes/Data/.Spotlight-V100
1082    /Volumes/NTM/.Spotlight-V100
183     /Volumes/fast/.Spotlight-V100
MacBookPro:~ bmike$ sudo du -sm /Volumes/*/.Spotlight*
1419    /Volumes/Macintosh HD/.Spotlight-V100
4273    /Volumes/PassportAir/.Spotlight-V100
4567    /Volumes/Retina/.Spotlight-V100