Issue #1:
...is that one of the other boards receive fine but will not let the radio go in to transmit. When I key up (mic, send, CW key) the radio just stays in receive.
I'm assuming that reseating the boards hasn't helped,
since you have tried both in the radio (sometimes that
clears a bit of corrosion on a connector). And that all
of the jumper cables got plugged in correctly.
In that case, the best way to trouble-shoot it is to
measure voltages along the T/R line on both boards
and look for a difference between them - that should
narrow down the problem pretty quickly. (This might
be easiest if you can put each board in a radio and
have them functional at the same time, but could
be done by taking a set of measurements, swapping
boards, and taking another.)
In general, this is a good procedure when you have
one good board (or radio) and one bad one.
Issue #2: The tuner "works" but on some bands with the tuner engaged I get only like 25-30 watts out...
I know you said you fixed this problem, but one thing
I discovered with my radio is that the tuner isn't always
very efficient. It has two motor-driven capacitors and
a band-switched coil in a T network, and actually can
match a fairly wide range of impedances, at least on
some bands.
But
after doing some testing, I discovered that, with
some loads that the tuner would match, a good manual
tuner gave me 3 dB more output to the antenna. That
means that over half the power is being dissipated in the
tuner, which probably means it is going to overheat with
any sort of extended use.
So, while it may have a fairly wide matching range, that
doesn't mean that it will always be efficient, even when
it can get a good match.