actually it sounds like we are doing pretty much the same thing. I use paypal file (or amazon file) -> excel (also handles currency) -> bigred importer -> quickbooks
Like many, becuase I was familiar with Excel, I started off using excel to 'manipulate' the data into a format that Transaction Pro Importer would be happier with...but it got unwieldly very fast (way too much manual effort). MS Access is the way to go ...alas, I didn't know a thing about MS Access, so it took a while to learn, baby steps etc (but there are heaps of youtube videos& dedicated forums).
There's a major (& I mean MAJOR) win to using MS Access vs. Excel....you end up with your own database that you can query in any way you want ...therefore any scenario you need quick stats for, it's do-able (& quickly) in Access.
Incidentally, it's better to use Linnworks as the ultimate 'source' of your data, as it acts as a front end to collect all your data from several channels...meaning one export has *all* your sales data (rather than you having to export paypal, then export amazon, then your own website etc.etc). If you are having to duplicate work (as you are at the moment, 1. Export Paypal. 2 Export Amazon etc), then that's a time overhead due to inefficiencies ....& they are big no nos for any business (especially small ones)
If Kashflow doesn't work for you (& I'm doubtful it will, once you start having several channels & use multi-currencies, the list of solutions gets less & less - when it comes to cohesive accountancy software that meets the needs of small e-commerce business, you'd think we were still in 1999!)....then IMHO you really ought to look at using something like MS Access vs. Excel in your present data flow.
As an aside, I realise that 'cloud' is the present craze...& yes there are many advantages...but I don't like putting my eggs in someone else's basket....I'm also of the opinion that all these cloud offerings want you to get pregnant with them, so that you can never easily leave...then the subs go up. A sub here, a sub there...it's the absolute scourge of starting /running a business...everyone wants a piece of you....& cloud subscriptions are the ultimate for this. Give it a year or two, we'll have 'cloud mis-selling' scandals!