Repairing Registry And Imaging Versus Recovery Partition

I have a Samsung laptop running windows 7 64 bit. I primarily use a non-administrator account. I got some malware a few days ago. Malwarebytes and MS security essentials seem to have cleared that up, but everything is still running slow in it.Additionally, the malware deleted all the shortcuts from the start menu (S.M.A.R.T. rogue antivirus, I deleted the temporary files before reading that was where the shortcuts were moved to)The administrator account is not suffering from the slowdown, everything seems fine in it. I made a windows repair disc using it.Partitions: there are four right now, windows (100mb), C drive (100gb), D drive (350 gb), and a recovery partition (15gb)1. I'd like to restore/repair windows 7 on the non-administrator account. From what I understand, the registry is likely faulty. I have little understanding of how to fix it, and no image or backup from before the malware infected. My data files are backed up to an external hard drive. I'd prefer to keep the programs registered and installed. I'm interested in dual-booting ubuntu. As the maximum of 4 partitions are assigned, I'd need to remove one of them. I've created a disk image of the system and C partitions onto an external hard drive (using Macrium Reflect). The data files are also backed up, either on that disc or on different clouds. I'd like to confirm that having done this, and having a windows repair disc, it's safe for me to use the recovery partition for ubuntu.