Hello
Firstly you may have unfortunately misinterpreted the crank clearance as it is 0.03 to 0.05mm, not 0.003 to 0.005 what evers, thous? I personally shim cranks tighter, to zero to 0.01mm on the basis that it is only going to get slacker when it gets hot. The crank is also more likely to spread with the factory setting. Basically as long as the rod bobs up on it's own when the cases are fully tight then it is not to tight. You have used none standard angular thrust mains, which in principle is okay, however I would definitely close up the side clearance towards zero otherwise the bearings will not work at there best and may lead to much movement in the bearings. Note bevel twins are shimmed to zero with similar bearings.
As for the gearbox, the design of the gearbox with an input and an output shaft doesn't lend itself to shimming like some other box's. Basically the shafts (and the fixed gears) are positioned by 2mm end shims, the other end is responsible only for the end float of the final gear. Generally speaking if you put the shims as per the parts book 95% plus of all gearboxes will work fine. I suppose somewhere around 0.2 to 0,3mm would be ideal for side play of a gear. Unless you have sufficient extra clearance to fit a 0.3mm shim or larger don't bother, as it will only spit it out! With a 5 speed narrowcase, I would avoid shimming the output shaft to any extent as the side play allows oil to lubricate the bronze bush which the output shaft in the four upper gears spins in. It should be noted that side play is necessary in all gears to allow good lubrication.
Okay, if you have time and the patience, sometimes you can make gains with careful retrospective shimming, but if you study the box hard enough most of the time you are making one thing worse to make one thing better! On this subject, there are various tolerancing errors in the gearboxes and you can't make it perfect by any amount of shimming anyway. Shimming the selector drum tighter will normally just result in worn out forks (from my observations of engines stripped) as the box relies on an element of float in the drum to allow all gears to engage correctly and not load the forks. Certainly 0.5mm is not to much slack for the drum and I have seen greater with no issues. The selector forks are there to guide gears to engage so an element of float should not matter. The dogs are there to hold the gear in, so if the dogs are rounded, using the fork to hold the gear in place is a work around not a solution! I once found a race engine with no side shims on the drum with at least 1.5mm side play and amazingly the box had been working perfectly. So this kinda supports my theory, not that I would recommend that much float
Best Wishes Nigel
