I assume you are putting the radio into Data mode. You do this by tapping the SSB switch and then pressing it again. For example, if you tap the switch to go into USB mode, press it again and the radio should go into USB-D mode. Unfortunately, this is not well explained in the IC-7410 manual.
I also assume that you are using the internal USB sound card and are connecting the radio to your computer using a USB cable. Note that if you aren't doing this, you should as it makes operating sound card digital modes much easier. Download the drivers from Icom's web site and install them before connecting the cable.
As for your menu settings:
38 -- I would leave this off all the time. You really don't want to squelch the audio going out to the USB sound card when you are operating in a data mode.
39 -- Adjust this in conjunction with the drive level in fldigi to get the proper ALC indication (none) when transmitting in data mode. It can be left where it is when operating in voice modes with the microphone.
40 -- This is the source of transmitted audio when not in USB-D or LSB-D modes. It should probably be set for MIC or MIC,ACC all the time.
41 -- This is the source of transmitted audio when in USB-D or LSB-D modes. If you are using the internal sound card, it can be set to USB all the time.
42 -- Leave it at whatever baud rate works with your rig control program. If it works with fldigi at 19,200, then leave it there all the time.
43 -- Leave it at the default (80h) all the time.
44 -- You can leave it on all the time, though some rig control programs prefer it to be off. If you aren't using an external tuner or amp that is controlled by CI-V, then I'm not sure this setting matters.
45 -- If your rig control program is connecting to the radio over the USB cable, then leave it on CI-V all the time.