I'm not familiar with the insides of a tr6 engine, but if i were you I would do as these fine gentlemen have suggested. if you are worried about the valves, try installing them in the appropriate locations according to the felt marker numbers. (your guy has marked them like this because he has matched each valve to each guide for fitment, also each valve to each seat for fitment and then finished by setting the installed height for each one). then lap each one quickly. then do an installed height check. if they are good, just go with it. don't think too much into it, you're not going racing right? just cruising the back roads on the weekend? i assume that if you were going to do some high rpm stuff then you would have taken your parts to somebody reputable for that application. the parts would have come back with all new stuff and look like they are new. those guys have to warranty their work, to a point, so they don't want to use any marginal stuff, and they want to fully assemble it so they know what the heights are, the spring tension specs etc. since yours didn't come back clean, or even assembled, we have to assume the machinist was giving you what you asked/paid for. sound correct?
if you are still worried,
if you lap the valves, check to see that there is a lapped ring all the way around the valve seating area and also on the head seating area. that way you know they are touching the seats all the way around. the ring should be roughly the same for all the intakes and also the exhausts. the intakes and exhausts will be different widths though.
take a look at the actual valves. check them against engine specs to see if they have enough margin.
then check for stem wear, galling marks or other defects. compare the stem measurement at an unworn spot compared to the worst worn spot. use a micrometer, not a vernier caliper.then compare that against engine specs sheet.
then check the area where the keepers ride to make sure that area is in good shape. you don't want to drop a valve because of a failure there. if there are burrs in that area then you may want to replace the valve and check the keepers closely, or just install new ones.
then check the keepers for wear.
then check the spring retainers for wear.
then check the valve springs for tension at installed height. or have it done. you can get away with shims to bring old springs back to within specs, but if parts are so cheap, why not replace them?
then check the valve guides for wear. make sure they are clean when you do this step. carbon in the guide will give you a false reading. that is why shops hot tank engines before they do any measurements.
then check the installed height against the spec sheet.hastings used to make a tool for this. it is like a piece of tubing threaded into another piece of tubing. it had a little set screw for locking it once set. it could be placed where the spring seat is and then a small straight edge could be used accorss the top of it against the end of the valve stem. you simply unscrew the tubing to expand or collapse the tubing untill it is the same height as the valve stem. then lock it and remove it and measure the length of the tube. that is the installed height of that valve. all the valves should be the same, intakes may be different than exhausts but all intakes should be the same as well as all exhausts. your guy probably already did this, or you could check with him at least.
then check the rockers and shafts or rockers and balls/pivots or whatever configuration you have there. check the rocker area where they contact the valve stem tips. make sure there isn't a divet there. check the pivot areas on the rockers for wear. check the end where the pushrod contacts for wear. check the pushrods for wear and straightness (roll them accross a clean sheet of glass or a "for sure" straight piece of steel). if the pushrods are hollow and are an oil gallery for the rockers, then make sure they are clean and clear inside. check the shafts, if applicable, for wear and proper oiling. if they are hollow make sure they are clean inside.
check the lifters for wear and/or pitting/cracking on the contact surfaces.
check the cam for wear and pitting/cracking on the contact surfaces
I could go on, but it should all be outlined in the engine manual. this is starting to look like a small novel, so I will stop now.