Sounds like you may've gotten a bad foreman -- even the best of companies
sometimes hires a joker who screws up a few jobs before getting the axe. The
acid test is going to be how well the company "makes it right".

Now, here I'm assuming you had the bed layout done *before* the bid was made (so
that the company was able to properly design the layout), and that you had made
it clear *at bid time* where you wanted the controller (it's somewhat difficult
to just randomly place the controller -- ideally it's relatively close to the
valves, which in turn are usually relatively close to the incoming water
supply). Unless there is a good technical reason why the controller is where
is it, I'd make 'em move it to where you wanted it.

Making the heads higher is pretty trivial -- it's just a matter of changing out
the riser. Maybe they just wanted the heads flush until the mulch was laid
(having all those heads sticking out is a recipe for breaking heads and risers).
OTOH, it could be the foreman is scatterbrained. And, of course, it begs the
question as to *why* you are watering your mulch (which just leads to the mulch
rotting faster), but I digress...

The head coverage is a different kettle of fish -- 100% head-to-head coverage is
the absolute minimum standard, so it needs to be brought up to that standard.
Assuming the design layout had 100% head-to-head cover (he *did* do a design,
right?), then something is funky. Perhaps the water meter needs to be upsized
to allow more flow, perhaps your local static pressure is lousy (although he
should have checked with the city as to the minimum static pressure), maybe
there are just some clogged heads or lines (very likely). In any case, it
needs to be made right.

It's pretty early to be talking about going to court. A company usually
doesn't develop a good rep just randomly, so for now I'd give them a change to
fix the problems.

Good luck, and don't back down!