what is your O/S ? hardware specs and ingame and video card settings, what cpu gpu ram vram % usage when you got those problems ? happening single player or multiplayer ?
Also if you are sure the problem is caused by input lag there is some ways to reduce input lag to a minimum with a fps limiter under the monitor frame rate.
if this work for you and you don't want to use RTSS , you can try the nvidi inspector frame rate limiter, with ingame vsynch on
or edit the startup.cfg game file frame rate line, like ( fps_limit = 59.593 , note this number depend of your accurate refresh monitor rate if you followed the guides above ) with the NVidia panel vsynch ON.
all that said, I got the feeling with 400ms lag mean you got other problem than just input lag, and there is many tweaks found on the net to reduce latencies cause by drivers, bios setting like hyper threading on or off or high precision event timer on or off and the bios cpu setting like the c-state or the intel speed step etc.. , or your window settings like the power plan to high performance , the system timers or the mouse pointer precision etc...
just do some search and there is many good guide to optimize your system, if you do, do a restore point before and tune your system .
I got a modest 6600k running 40-60% usage with only 8g ram and a gtx 970 running 40-75% and I run all ingame setting to max, AA transparency ON with moderate density career and PWCG air density to high and ground to medium, on a monitor overclocked to 75HZ and it keep a 75fps all the time with as much or better smooth gameplay than any il2 box video I can find on youtube , unless someone got a really weak hardware the sim should run smoothly on anyone system if mine can do like this , but you got to take time to seek and find
what slow down your pc.
In my case right now with all my tweaks done, only to switch on bios high precision event timer setting or switch window power plan to power saver make the game unplayable from the start, crazy lag and stutters, feel like 2-3 fps, maybe just this can help you ?
some essential tools for me to run il-2 box not just playable but naturally smooth (know many need to run as administrator to run ) also doing web search with those tool names can lead you to good guides to understand and tune your pc:
to check what cause latencies on your system
this tool below is free and easy to use, it run on the back ground and run all the time on my system and it is automatically adjust with the window power plan I use
the best tool if you want the best frametimes as possible
you may not want to use this but overclocking my monitor refresh rate from 60 to 75 make my frametimes shorter and mitigate effect of small frametimes spikes when I use the zoom in game.
MSI_util_v2.exe found on this page below, (that can be find here to tweak system interrupts ,this one help me a lot to reduce video and audio latencies) run as administrator to work
to monitoring hardware cpu gpu ram and vram and lot more
sorry for the long post, but you asked for advices and there can be so many more reasons having good fps but lag ,frame skipping or stutters problems, I just gave you some leads
You like it or not you may have to do some search/work to get the most of your pc and really enjoy the beautiful graphics in il-2 BOx .
good luck with this