New bottom bracket, asymmetric cranks I am seeking help for a "dilemma" I have with my upgraded bike.
I have an old KTM Ultra Line (2004) that I have upgraded with a new chain wheel (FC-M590 48.36.26t), a Shimano BB52 bottom bracket (previously a Shimano UN26), Shimano Deore XT M772 Shadow (long cage) rear derailleur, a new freewheel body and a Sram PG990 cassette.

Having a bottom bracket shell 68mm wide, and a band type front derailleur, I have installed one 2.5 mm spacer on the left side, and two 2.5 mm spacers on the right side, as specified by Shimano's installation instructions.

Before the upgrade the bike was fitted with a square taper bottom bracket Shimano UN25 ( 110 mm axle width ).

Restoration work continued with new ball bearings for both front and rear hubs, and new cones and axle for the rear hub. Then I brought the bike to a local bike shop to replace brake and shifter cables, adjust the new chain (KMC X9) and check the wheels.

Then the mechanic told me he had to swap the spacers on the bottom bracket because otherwise the chain line wasn't centered and that should have put more stress on the rear derailleur.

When I went back telling him that the two cranks are now asymmetric with the rear crank far more near the frame than the left crank, he told me that the chain line it's that matter and I should not worry.

Yeah I should not worry but I feel the difference on my legs (using cleats on the pedals) and after just 20 km my left leg began to hurt.
What am I suppose to do? I will try to swap back the spacers as per Shimano's instructions, how can I judge it that put some stress on the derailleur?

I have taken some pictures and videos, here: https://onedrive.live.com/?authkey=%21AE3dvdm3sIVKh9c&amp;id=9BC36237EA980F31%21136&amp;cid=9BC36237EA980F31
Put the spacers back in and see how it feels. If it feels better and your gears a shifting well enough for you, leave them in.

As @Daniel says, chainline is not as important as some believe. In a perfect world, you get the chain line right and never, never, ever, cross the chain. But just like the movie, sometimes you just have to cross the chain, and hell does not freeze over. 

New MTB's are going to 1x11 (and 1x12), and the cassettes are wider than 9' or 10's. If chain line was so critical, these 1x11 would never work. 

If your chainline is badly out, you may have problems getting shifting to work as smoothly as it should, your chain may wear a little quicker than it would, and the little cogs on the derailleur may wear out a little sooner. Notice the word may, and its a a very small if it does, and very debatable.....