How long have you had her? How many times has she been tested for Johnes? One clean test isn't a very good picture at all, as known positive animals may give a neg result if they are able to keep the Johnes 'at bay'. If you have a few years of negative ELISAs, then you can trust them... but otheerwise, it may be worthwhile to do a fecal Johnes culture.
Severe cocci loads or intestinal disease when young can cause permanent scarring of the intestine and SEVERELY decrease an animals' ability to absorb nutrients. (Thickening of the intestine and scar tissue accumulation is the same reason Johnes causes animals to waste away, too, just as an FYI) This would have happend as a young kid but can affect them their entire life in their ability to utelize the food they eat.
If she were mine, I'd probably try an extended dry period and feed her a fairly rich diet through her dry period. I'd probably cut it back to a normal pregnancy ration about amonth pre-kidding to keep the kids from getting super huge. I'd consider using replamin on her as well.
The problem with increasing carbs in her diet is that she will be prone to acidosis so you'll have to be sure she gets baking soda free choice - and if she slows in appetite, drench her a few times with baking soda. Too much fat in the diet makes it hard for them to digest PLUS polyunsaturated fats are toxic to rumen bugs and must undergo biohydrogenation in order for them to be utelizeable - this is not a problem unless you REALLY over feed them because there are only so many enzymes and they can only work so fast.
What's her diet like, and what have you tried in the past?