To get a higher appraisal amount, I would like to repaint the house in order to make the house cleaner.Is there a solution that would fix the smoke/nicotine stained walls and keep it from being stained again?

The thing is, properties have issues that pop up after inspections, kids break in and repaint a room for example (LOL) so, yes, justify your offer.

I plan to repaint all of my rooms to a neutral color.My concern is, would I regain the money put into installing the floors plus some?

Requires some rehab, paint, bathroom I can place new tiles, new vanity, repaint the kitchen or maybe get a new one, nothing expensive, around 1500 plus install.

Otherwise, you can clean, repaint, repair missing hardware, and add storm windows and make them just as efficient as replacement windows - but a bigger hassle for sure in the future. 

I don't personally have any experience with buying a multi via FHA, but I can tell you from a seller's point of view ... having not dealt with the FHA inspection aspect before, I was amazed when my realtor advised that I'd need to, for example, repaint the eves of my house because some of the paint was flaking off, and that FHA would likely flag it and not issue a mortgage, because of something as minor as flaking paint ... the eves were freshly paint 5 years ago, mind you, so its not like they had been neglected for 20 years.

Expenses were low, tenants paid utilities, mowed the lawn, shoveled the snow and stayed for 5 years, meaning no repainting, etc. and no vacancy.I decided to sell, because it was away from other rentals that I owned and managed. 

Building could use a repaint, a few awnings need repair, and landscaping could use some help.

When we bought the place It had brand new carpeting and paint (probably the cheapest they could find) my question is how often should I expect to have to repaint and put in new carpeting and when I do should I follow Fannie's example and go for the cheapest as well?

there is a difference in negativity and reality.. that's all I am pointing out.. full blown rehab construction is fraught with Risk.. we deal with it every day.. even new builds guys make boo boo's  I walked in one of our new builds same floor plan we had built numerous times and the window is too low won't pass inspection.. cut it out.. cut out siding replace replace siding patch the dry wall re paint.. etc etc.The other major thing is that rehab contractors are not new build subs.. your subbing each trade out .. your rehab contractor is usually a different breed and one that can actually run a whole job for you is usually doing work for owner occs and  charging for it.. what YOU need to pay to make a profit brings you down to the guys and gals that need utmost supervision..