repairing registry and imaging vs recovery partition

I'm confused about the pros and cons for recovery options.

Brief background:

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. What would be the best way to do this?

2. 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.

At this point, my head is spinning from all the new information. I'd thank anyone in advance for advice on any tips to restore windows and to confirm that I can reassign the recovery partition.

A windows repair disc is not the same as the manufacturer recovery discs.

The latter are usually run off from a program the oem has provided - under the start menu probabaly.

It uses the recovery partition to make the discs. Make sure you have those first if you are getting rid of the recovery partition

I couldn't find any samsung recovery option. But it sounds like with a windows repair disc, and the recovery partition, the windows partition, and the C partition imaged to the external, that I should be safe to remove the recovery partition?