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For what its worth - if you are having issues on roads, then your form need looking at. Roads are the ideal place to run barefoot due to the regularity of the surface, if you can run trails but not roads then you are presumably using the softer trail surface to compensate for the lack of shoe cushioning rather than your form.

The best way to transition to minimalist is to go extreme rather than gradual. Your body will quickly tell you if you aren't doing it right! (But obviously build up gradually - extreme as in stripping back the footwear, not in mileage!)  If you still 'need' some cushioning then you are still relying on it for shock absorbtion and all going minimalist is doing is increasing your chance of injury as you have reduced protection but not perfected your 'new' form.  You will get away with it for shorter distances - but not so good as you ramp up mileage (same as for racing flats vs more substantial shoes for training for a heel striker.)

I run in VFFs and Evos - I get noticably more joint aches in the Evos as they have a more substantial sole and my form suffers because I can get away with being sloppy (I use them as they have passable rock protection, I run trails as I hate road running, not because I need to for the surface).  In my VFFs I feel much lighter and am still concentrating on where my feet are going by the end of a 13 miler.

A meta analysis (10 trials on just shy of 4000 patients)  of  glucosamine+chondroitin by the bmj

http://www.bmj.com/content/341/bmj.c4675.full

Conclusions:

Compared with placebo, glucosamine, chondroitin, and their combination do not reduce joint pain or have an impact on narrowing of joint space. Health authorities and health insurers should not cover the costs of these preparations, and new prescriptions to patients who have not received treatment should be discouraged.

How much have you increased your calorie intake by to compensate? 5 extra miles is in the region of 500 kcal, give or take a bit - over a whole week. Possibly slightly less if you are metabolically efficient.  Thats 70kcal a day - maybe less; not a lot to compensate for.

As per the previous post - if you are tracking your calorie intake to 70 Kcal per day I don't think the armchair PhDs here are the advice you need...

I do nearly all my running offroad and anything up to 13m will go minimal (VFF or vivobarefoot) anything over I go for 'flatter' trail shoes.  If anything offroad is better as you have less of a tendancy to overstride as you don't want to 'commit' each footfall so much in case it isn't stable.

The one bit of advice would be to bend your knees.  (if you read Gordon Piries book- avail free as a pdf on the internet if you look.  He was a distance runner in the days before trainers as we know them so minimal was the only option).  He says: 

Let us start at the very beginning, with the person standing to attention in bare feet. Raise 

yourself up onto tiptoes, and overbalance forward. You must take a step forward to keep 

from falling over. From the position which results (it is impossible to step forward onto 

the heel), you should begin to run at a slow velocity - but with very light, quick steps - 

making sure to feel the stress on the toes. The runner's legs should remain flexed at the 

knees. A feeling of "sitting" with the seat down "like a duck" is employed with the body 

upright. An athlete who runs correctly will actually appear to be shorter than other 

runners of the same height who are not running properly. By keeping his knees flexed and 

by landing on the ball of the foot on each step, and with the foot beneath the body, the 

runner will spring along very quietly. As the weight of the runner's body rides over the 

foot, the entire sole will rest flat on the ground - do not remain like a ballet dancer on 

your toes throughout the weight-bearing phase. Alison Roe did this, and was constantly 

injured.

Basically - bend your knees.  A fully shod heelstriker locks the leg and relies on padded shoes to cushion the blow.  A barefooter relies on tendons and muscles to do the same job.  \if you are landing mid-foot you are half way there, but if your knees are still locked you will have issues.

All sorts of unfamiliar aches and pains when transitioning to barefoot/minimalist, knee pain isn't a common one.  How short is very short regarding both run distance and stride length? (I consider 3 miles too short to bother going out for while to some people 5k is a target goal!).

Have you tried actually short periods of barefooting to see if you are carrying more bad habits than you realise?  Smooth concrete is actually the best for this as grass will still allow you to heel strike if you do it smoothly enough.  And if your form is good concrete is actually fine to run on - if you get hotspots there is actually a guide to tell you which form problems cause which blisters. 

Count your cadence - should be 180 steps/pm or so, this will help determine if you have shortened your stride enough.  Quite a few youtube vids on barefoot form - it is quite different and takes a while to get used to.

Your best bet however is to post or search the barefoot forum on the us site (.com) as there is plenty of advice there (but a few zealous anti-shoe of any desacription types...)